The presidential commission studying the stock market collapse is considering changes in the way stock and futures markets are regulated as well as in the New York Stock Exchange's specialist trading system.

The regulatory changes under consideration are intended to overcome conflicts between the Securities and Exchange Commission, which oversees stock trading, and the Commodity Futures Trading Commission, which supervises futures trading, including trading in stock index futures contracts.

Stock index futures contracts give investors the opportunity to bet on the future movement of stock prices by purchasing contracts that represent broad stock market averages, such as the Standard & Poor's 500.

Meanwhile, New York Stock Exchange officials yesterday criticized a proposal by the presidential commission headed by investment banker Nicholas F. Brady to put daily limits on the amount that stock prices can move. The limits would be designed to diminish stock price volatility, which hit its peak in the 508-point drop in the Dow Jones industrial average on Oct. 19.

Brady emphasized yesterday that the stock price limit proposal is only one of many options the panel is considering.

The close relationship between trading in stock index futures and stocks in the October market collapse, and the problems caused by having two separate regulatory agencies and different congressional committees overseeing the agencies, has led money manager Robert Kirby, one of the five members of the Brady Commission, to suggest the need for a "supercommittee," with authority over both markets and agencies.

"I would favor some kind of system where you began with self-regulation {by the exchanges} and you had a supercommittee up there that oversaw everything," Kirby said. "You need better coordination or some big brother up there above both who says, 'Look you guys, what you are doing doesn't make sense.' "

Kirby ruled out an outright merger of the two agencies.

"It is impractical to say we are going to put New York {stocks} under the CFTC or Chicago {futures} under the SEC. That is just plain political reality," he said. Merging the agencies, Kirby said, would be "kind of like merging the Iranians into the Iraqis."

Kirby said the committee to oversee regulation of stocks and stock index futures should not be a congressional committee, but instead a panel made up of officials of the SEC, CFTC and others with an interest in the matter. Brady confirmed that his commission is considering the supercommittee idea.

The current system whereby different Hill committees oversee the SEC (stocks) and the CFTC (stock index futures) creates jurisdictional problems, Kirby said. "Everybody has somebody's point of view tattooed on his rear end," he said.

The Brady Commission will meet Monday to begin formulating conclusions on what caused the stock market drop and what regulatory changes are needed, and plans to submit its report to President Reagan by Jan. 4. Next week, the panel will consider arguments it has heard from Wall Street officials, including New York Stock Exchange Chairman John J. Phelan Jr., that a coordinating committee is not enough.

Sources said Phelan told the commission that stocks and stock index futures should be placed under one regulatory roof in Washington.

"The products are so inseparable in terms of one impacting the other that to have separation of agency oversight doesn't make much sense," NYSE Executive Vice President Richard Grasso said yesterday.

One way to accomplish this would be for the SEC to regulate stock index futures as well as stock and stock options markets, with the CFTC continuing to regulate traditional commodity futures. However, officials of leading futures exchanges and the CFTC oppose such a plan, arguing that the current regulatory structure makes sense and worked well in October.

Sources said Phelan also has urged the Brady Commission to suggest that the Federal Reserve Board set margin requirements for both stock and stock index futures trading. Under current regulations, the Fed sets margin requirements for stocks, which permit investors to borrow no more than 50 percent of the funds used to purchase securities. The futures exchanges set margin requirements for stock index futures, which have been raised recently to about 16 percent.

Charles M. Seeger III, vice president of the Chicago Mercantile Exchange, said margins on stock index futures are actually good faith deposits and serve an entirely different function than margins on stocks.

Seeger said that giving the Fed authority to set margins in stocks and stock index futures "implies that during the cataclysmic events the margins in the futures world somehow didn't work, that somehow financial integrity was jeopardized, when it remained intact and no customer lost a penny."

Kirby said the need for additional capital may mean the end of the days of the small specialist firm. Specialists assigned to each stock have the responsibility for maintaining orderly markets by buying when there is an absence of public buyers and selling when there is an absence of public sellers.

Kirby said the specialist firms need to meet higher financial standards and need to have guaranteed lines of credit to raise cash in market crises. He said the problem with small specialist firms was that they didn't know on Oct. 19 whether banks would lend enough money to help them complete anticipated and actual stock purchases.

Grasso, commenting on a proposal being considered by the Brady Commission to put daily limits on stock price movements, which could make the specialists' job more predictable, said the move could hurt investor confidence and drive trading to foreign markets.

"It is certainly nothing we would consider a front-burner strategy for dealing with the issues of volatility and structural reform," Grasso said.