President Reagan yesterday signed the final executive order, and the Treasury Department issued regulations, to carry out the agreement with Iran that set the stage for settling claims against Iran and freeing the hostages.

In doing so, the federal government suspended claims pending against Iran in U.S. courts that might be referred to the international arbitration commission and nullified court-ordered attachments or Iranian property.

The regulations also made clear that a transfer of approximately $1 billion of Iran's assets is likely to be delayed nearly five months more by legal challenges to the government's authority to agree to some of the terms.

"We've always assumed that there would be few transfers until litigation was resolved," said a Treasury official, adding that the Iranians expected such a delay. The regulations require that Iranian bank deposits in the United States and other funds and securities be transferred to the Federal Reserve Bank in New York as soon as possible for transfer to Iran and into a fund that will be used to pay claims as they are settled by arbitration.

But the regulations also spell out that the United States will not seek any criminal or civil penalties against banks and other who fail to make the transfers.