ALBANY — When Edward Cardinal Egan sat down with Sheldon Silver this week to implore him to give parochial schools more financial help, the Assembly speaker waylaid the New York archbishop with a little-known fact: His house’s budget includes more money for nonpublic schools than what was proposed by Governor Spitzer.

Apparently without prior permission from the city’s teachers union, Mr. Silver stuck in a provision that would deliver $39 million in aid to private and parochial schools to help them pay for special services mandated by the state, such as keeping attendance and conducting standardized tests. With costs increasing in recent years because of new state mandates, Mr. Silver is proposing to help the schools make up that difference.

“The cardinal sat here and said to his legislative aide, ‘How come I don’t know about this?'” Mr. Silver told The New York Sun in an interview.

The Democratic speaker has a reputation among school choice and parochial school advocates in New York as their biggest obstacle in Albany.

The Assembly’s one-house budget, which represents its starting point with negotiations with the governor and the Republican Senate, did not improve Mr. Silver’s standing. Advocates say Mr. Silver once again transcribed demands made by the United Federation of Teachers into statutes.

The Assembly, for instance, eliminated Mr. Spitzer’s $25 million plan to give parents who pay for private or public school tuition $1,000 tax deductions. Worth on average $68 a year, the money was not a windfall, but for private and religious school advocates, the deduction represented an important precedent for using state funds explicitly to help families pay for private tuition.

The unions opposed the measure, and Mr. Silver took it out. Instead, he proposed expanding a tax credit program that gave families $330 for every child ages 4 to 17. The Assembly’s bill includes children younger than 4.

Charter school proponents say Mr. Silver chopped up Mr. Spitzer’s charter school plan almost beyond recognition.

The governor’s budget bill authorized 150 more schools, allowing New York City’s schools chancellor, Joel Klein, to open 50 of his own. The speaker’s budget allowed for only 50 new schools and gave Mr. Klein no role in their creation. While lifting public school aid by a record $1.45 billion, Mr. Silver proposed cutting charter school per-pupil funding by more than 30% over the next three school years.

Bowing to another request by the United Federation of Teachers, Mr. Silver also included one provision requiring that charter schools be unionized if they exceed 250 students and another that would make it more difficult for the schools to fire teachers.

The speaker told the Sun that he is not ideologically opposed to using state money to aid private schools, citing the $39 million in funding as evidence. Private school lobbyists, however, point out that the schools are legally owed the money; they say the governor’s office would have eventually reimbursed them once its budget unit determined the cost of the new attendance requirements.

Mr. Silver dismissed Mr. Spitzer’s $1,000 tuition tax deduction plan as comically miniscule. The speaker pointed out that he is proposing to give parents five times the tax break without restricting how they spend the money. In his view, if the Legislature required that parents spend the money on private education, schools would waste the benefit by raising tuition.

Mr. Silver, however, does not hide his suspicion of charter schools, which are publicly financed schools run by independent groups under contract with state agencies. The state has about 28,000 charter students — about 1% of the public school population — a number that will remain flat unless the Legislature authorizes more schools.

Charter schools, Mr. Silver said, belong “in a structure where they fit in, where the community accepts them. When they begin to disrupt existing schools, they don’t belong.”

He justified the funding cut on the basis that charter schools are more adept at thriving on shoestring budgets. “Charter schools profess to be able to educate children cheaper than public schools,” Mr. Silver said. “That’s their no. 1 claim, so we are asking them to do that.”

Mr. Silver said he was not moved by the Bloomberg administration’s insistence that more charter schools would strengthen the city’s school system by injecting new ideas and fresh blood.

Mayor Bloomberg and the chancellor “came to this Legislature and asked for mayoral control,” he said. “We gave it to them. I don’t understand their argument that we need somebody to compete with so we can improve the performance in a competitive mode.

“They’re in charge. Now they are saying they need somebody else to improve the system? I don’t understand. It’s obviously more complex than they thought,” he said.

A spokesman for the Department of Education, David Cantor, said in a statement that Mr. Silver “shows little respect for the thousands of families who are being served by — or wait years to get into — our city’s outstanding charter schools. It’s unfathomable that he would deny underserved children choices that allow them to receive a good education.”