NEW YORK -- Hefty profits from innovations in mortgage securities illustrate why the Reagan administration should quickly stall the secondary mortgage market, a Washington attorney siad last week.

"The profits they're keeping from these new deals make it clear that the homebuilder is not getting the naximum benefit," said Bernard Carl.

Government agencies in the secondary market use predatory pricing, made possible by their credit advantages over the private market, Mr. Carl said. A former government housing official, he helped U.S. Treasury officials draft a controversial bill now under consideration.

The legislation -- still in draft form -- would establish special tax structures called Trusts for Investments in Mortgages, while limiting the use of government-related mortgage securities.

After leaking out last week, the proposals prompted widespread outcry from financial, housing, and real estate trade groups.

Officials of the Public Securities Association, for example, last week wrote President Reagan, strongly objecting to the bill. The securities dealers have supported the administration's desire to remove government agencies from the center of the secondary market -- but are objecting to the actual legislation's sweeping scope and effective date. Retroactive to Introduction Date

The draft bill would apply, once approved by Congress and signed of introduction. That would stifle as much as $12 billion in one affected form of mortgage security, the collateralized mortgage obligations, now in the works, predicted W. …