The Patrick administration on Wednesday proposed a series of cuts in state spending to close an estimated $329 million budget gap. The executive branch will absorb nearly $200 million of the cuts, but officials are also paring back spending envisioned by the recently passed economic development law, including $16 million targeted for so-called “transformative investments” in Gateway Cities.

Glen Shor, the secretary of administration and finance, said the executive branch will unilaterally cut $198 million from agencies under its control, withhold $25.5 million of the $82 million in spending contained in the economic development law, and take back $3.5 million from the Massachusetts Life Sciences Center. Shor said the administration will also seek legislative approval to cut $25.5 million in unrestricted local aid to cities and towns, $21.8 million (1.5 percent) from non-executive branch agencies, and $10 million from the Department of Transportation.

State officials said the $25.5 million spending reduction under the economic development law includes $16 million for a transformative development fund aimed at helping Gateway Cities and $7 million for brownfields redevelopment. Documents released by the administration indicated another $1.5 million would be cut from the transformative development fund under the unilateral cuts.

Mark Sternman, a spokesman for MassDevelopment, which administers the transformative development and brownfields funds, said the authority is still trying to nail down details about the cuts. He said the authority may have to scale back its plans but will continue to push ahead. “We’ll make the best of the situation,” he said.

Greg Bialecki, the secretary of housing and economic development, said on Thursday that the administration intends to come up with funds for the MassDevelopment initiatives, which will be phased in over several years. He promised more specifics in the coming days. “We believe there are other available resources to fund these programs,” he said.

The administration is grappling with a deficit brought on by an expected income tax reduction that will cost the state $70 million this fiscal year and fees and reimbursements that are coming in slower than expected. Shor said the economic development act also was approved by the Legislature on the assumption that tax revenues would be higher.

Shor expressed confidence the state’s budget gap will be closed, even though the Legislature in the past has frowned on local aid cuts in the middle of the year. House Speaker Robert DeLeo said on Thursday he would not support the local aid cut.

The Massachusetts Taxpayers Foundation is also predicting the deficit for the current fiscal year could run into the $500 to $600 million range. Shor said the Patrick administration had not consulted with Gov.-elect Charlie Baker on the cuts and had no immediate fallback position in case the Legislature balked at some of the proposals.

“We don’t have an alternative solution,” he said. “This is our solution.”