A Pentagon spokesman called on Moscow "to take immediate steps to de-escalate the situation."
The official gave no details on where the incursions took place or the goal of the action.
The flights come as Russia increases military exercises along the Ukrainian border.
On Thursday, the top U.S. military officer Chairman of the Joint Chiefs of Staff, General Martin Dempsey, spoke with his Russian counterpart.
Also Friday, pro-Russian separatists in eastern Ukraine detained a team of international military observers.
The separatists seized a bus carrying at least 13 people from the Vienna-based Organization for the Security and Cooperation in Europe [OSCE] near the town of Slovyansk.
The town's self-declared mayor, Vyacheslav Ponomarev, said the group was detained because a Ukrainian military official was traveling with them.
"The sign OSCE does not mean protection for an officer of the [army] General Headquarters. We found an employee of the army headquarters. After an investigation we will decide what we are to do," said Ponomarev.
The OSCE wrote on Twitter that it had lost contact with the German-led monitoring team.
The United States and the European Union are expected on Monday to impose new sanctions on Russian individuals, sources said, as the Ukraine crisis escalated with armed pro-Russia separatists seizing a bus carrying international mediators.
The U.S. State Department is condemning the reported abduction of an international observer team and its Ukrainian escorts by armed gunmen in the town of Slovyansk.
"If true, we strongly condemn this action and call for their immediate release," said State Department spokesperson Jen Psaki.
"Over the past week, we've unfortunately seen a rapid escalation in hostage takings by pro-Russian separatists. We condemn this repressive and cowardly tactic and call for the release of all hostages."
Pro-Russian separatists say the group was detained because a Ukrainian military official was traveling with them.
The interior ministry in Kiev said the detained group includes seven OSCE representatives and five members of the Ukrainian armed forces who were accompanying them.
On his Twitter account, Swedish Foreign Minister Carl Bildt called for the group's immediate release:
"Extremely concerned with OSCE inspectors being abducted in Eastern Ukraine. Including one Swede. They must be released immediately."
Meantime, a leading Russian military leader is voicing concern over the situation in southeastern Ukraine, the Interfax news agency reported.
In a telephone call, Russian Gen. Valery Gerasimov told U.S. Gen. Martin Dempsey that Ukraine has a "substantial group of forces" near the Russian border, which includes some troops intent on conducting sabotage.
Ukrainian forces killed up to five pro-Russia separatists Thursday during an effort to regain control of rebel-held areas.
President Barack Obama discussed Ukraine crisis Friday in a telephone call with French President François Hollande, German Chancellor Angela Merkel, Italian Prime Minister Matteo Renzi and British Prime Minister David Cameron.
The White House said in a statement that the four leaders agreed Ukraine had taken "positive steps" to uphold the four-party deal it signed in Geneva last week to de-escalate tensions, while Russia had "not reciprocated."
According to the White House, Obama said the United States is prepared to impose targeted sanctions to respond to Russia's latest actions, and all four leaders agreed to closely coordinate additional steps to impose costs on Russia.
Treasury Secretary Jack Lew said Friday that the next round of sanctions against Moscow will put more pain on the Russian economy.
"We are working with our international partners to make sure that when we do it, we do it in an effective way,'' Lew said on Marketplace, a radio show produced by American Public Media.
The development follows an accusation earlier Friday by Ukrainian Prime Minister Arseniy Yatsenyuk that Russia wants to occupy Ukraine "militarily and politically," as both Kiev and Moscow mass troops close to their mutual border.
Yatsenyuk warned Friday that Russia's actions could lead to a wider military conflict in Europe.
He told an interim Cabinet meeting that Moscow "wants to start World War III."
His comments came amid reports of fresh violence in eastern Ukraine, where pro-Russian militants continue to occupy government buildings in around a dozen cities.
A Ukrainian military helicopter exploded Friday on the tarmac of a base near the eastern city of Kramatorsk.
Some Ukrainian officials said the explosion was the result of a rocket-propelled grenade fired by pro-Russian militants, while others said it was caused by a sniper who fired a single shot into a fuel tank.
Ukrainian officials said Friday that they aimed to "blockade" the rebel-held city of Slovyansk as part of an "anti-terrorist" operation in eastern Ukraine.
Russian Foreign Minister Sergei Lavrov on Friday denounced Kiev's security operation to clear the pro-Russian militants, calling it a "bloody crime."
Russia has reportedly dramatically increased the number of troops deployed along its border with Ukraine.
A Ukrainian diplomat at the United Nations told VOA that Moscow has doubled its military presence on the border to about 80,000 troops.
Lavrov, for his part, blamed the West for raising tensions, saying Friday that the pro-Russian militants would only lay down their weapons if the Ukrainian government first clears out its own protesters in the capital.
Credit rating downgrade
Underscoring the effect that wider sanctions could have on Russia's economy, credit agency Standard and Poor's cut Russia's credit rating to BBB-.
The agency said it is concerned about increased capital outflows from Russia, and said the rating could be cut further if sanctions are tightened.
Washington has accused Moscow of failing to uphold the four-party deal it signed last week calling for all parties in Ukraine to lay down their weapons and vacate public buildings.
U.S. Secretary of State John Kerry said Moscow has not taken "a single step" to de-escalate tensions since the deal was signed in Geneva.
Seven people were injured overnight at a pro-Ukrainian checkpoint near the Black Sea port of Odessa when an explosive device blew up, police said on Friday.
Residents in the town have built several such checkpoints near the town aimed at stopping pro-Russian separatists entering from Moldova's breakaway territory of Transdniestria.
Interfax news agency quoted witnesses as saying a bomb was thrown at the checkpoint from a passing car, though this was not confirmed by police.
Transdniestria, home to Russian peacekeepers and Russian troops guarding a Soviet-era arms stock, declared independence in the early 1990s.
NATO warned last month of a possible Russian military grab for Transdniestria following its annexation of Crimea.
Ukrainian forces killed up to five pro-Moscow rebels on Thursday as they closed in on the separatists' military stronghold in the east, and Russia launched army exercises near the border in response, raising fears its troops would invade.
The Ukrainian offensive amounts to the first time Kiev's troops have used lethal force to recapture territory from rebels who have seized swathes of eastern Ukraine since April 6 and proclaimed an independent “People's Republic of Donetsk”.
Source: Voice of America