Alexander Zakharchenko and Igor Plotnitsky said in a statement that legislation giving areas of the Donetsk and Luhansk regions special status has been weakened by the amendments.
"We agreed to a special status for the Donbass within a renewed Ukraine, although our people wanted total independence. We agreed to this to avoid the spilling of fraternal blood," the statement said.
But Ukraine did not renew itself," it continued.
Rebels have pushed for revisions to the constitution to decentralize power, but argue that authority is still held by powerful businessmen.
A law on granting autonomy to eastern territories was approved by parliament Tuesday, but with a number of changes that have drawn sharp criticism from Moscow-backed rebels and Russia alike.
Foremost among the rebels' objections is a requirement for elections — to be held under Ukrainian laws — to take place before the special status can come into effect.
A Ukrainian foreign ministry spokesman said in an emailed statement that enacting the special status law without elections approved by Kiev would result in the legitimization of what Ukraine considers unlawful rebel governments.
Russian Foreign Minister Sergey Lavrov said Ukraine's parliament had undertaken a wholesale rewriting of the agreement.
"What comes out of parliament's decree is that only when these territories are led by somebody suitable for Kiev will the law on special status come into effect," he said.
"That is an attempt to turn everything that was agreed upon on its head."
Ukraine has also drawn anger from separatists with its plans to seek deployment of United Nations and European Union peacekeeping missions in the east.
Parliament voted Tuesday to back a formal request for the mission.
Zakharchenko and Plotnitsky said placement of a peacekeeping contingent had not been agreed at cease-fire negotiations concluded between the leaders of Ukraine, Russia, Germany and France last month in the Belarusian capital, Minsk.
"The manipulation of good intentions for coverage is another attempt to get out of the Minsk agreement," the rebel leaders' statement said.
A U.N. peacekeeping mission would likely need backing from all five permanent members of the Security Council, and Russia is almost certain to resist the move.
More than 6,000 people have been killed since fighting broke out last April.
Clashes have reduced substantially since a cease-fire was declared last month.