President Viktor Yushchenko vetoed the 2007 budget a week ago and returned it to parliament, demanding higher social spending.
Yushchenko said estimates of living costs in the budget, on which pension payouts are based, were too low.
The Cabinet, which had backed the original draft, criticized the president's move, and the sides held talks Friday. Yushchenko, pro-Russian Prime Minister Viktor Yanukovych and senior members of parliament then negotiated a new draft.
A total of 245 of 437 deputies voted for the new budget Tuesday.
But the presidential secretariat will recommend that Yushchenko not sign the amended budget law, its deputy head Arseniy Yatsenyuk told journalists.
He said the new version of the budget was also unacceptable to the Ukrainian people, and that parliament members failed to calculate the budget properly in five days.
Yatsenyuk said "the president's proposals aimed at protecting the less socially protected population were not taken into account, and this budget cannot be signed."
Yulia Tymoshenko, the leader of an opposition bloc, said the anti-crisis coalition and its government are provoking Yushchenko to veto the budget, as they are interested in taking it under their control.
"This budget has received no amendments. The budget crisis has reached its height," Tymoshenko said.
"They [the Party of Regions led by Yanukovych] will not seek to override the veto. It serves their cause," she said earlier, adding the party will blame all socio-economic problems on the president and the "orange team" which supports him.
