The Bank of England has refused to handle the second, $1 billion escrow account called for by the U.S.-Iran hostage release agreement, according to American government sources.

The bank's decision, the sources said, was based on a fear that political problems could develop over handling of the account.

The account is to be made up of once-frozen Iranian funds still held by U.S. banks. The funds would be used to pay American corporations and individuals whose claims are approved by a yet-to-be-established international settlement commission.

If the balance dropped below $500 million, the Iranians were to make new deposits to bring it back up to that amount.

The Bank of England's refusal has not yet interfered with implementation of the Jan. 19 agreement, but has forced American officials and Algerian diplomats, who have served as intermediaries in the negotiations, to look for a new institution that would be acceptable to the countries involved.

Meanwhile, it was learned from Iranian sources that officials of the Ayatollah Ruhollah Khomeini government are unhappy -- but not enough to complain -- over the way the Reagan administration is delaying implementation of the hostage agreement provision on the U.S.-based assets of the late shah and his relatives.

Under this provision, the U.S. government was to "freeze and prohibit any transfer of property and assets in the United States within the control of the estate of the former shah" after the hostages were released. In addition, a freeze was to be put on the assets of his relatives once they were legally served with papers that made them parties to Iran's lawsuit in this country to regain assets taken illegally.

Under Treasury Department regulations of Feb. 25, neither the freeze on the shah's estate nor his close relatives will become effective until Iran provides the treasury with proof that they have been made defendants. A suit has been under way for more than a year in New York with Iran's lawyers arguing, unsuccessfully, that they had in fact served the ousted shah with legal papers before he died.

There is no indication when a ruling will come down, but if it is appealed the matter could be tied up in court for years, effectively preventing for that time a freeze on the assets.

An administration official said the U.S. regulation was drafted based on the U.S.'s interpretation of the Jan. 19 agreement.

According to several sources familiar with the negotiations that led up to the release of the 52 hostages, Bank of England officials had said even before the agreement was signed that they would not handle the second escrow fund called for in the settlement.

The British institution finally agreed to have its name used in connection with the second account, sources said, to prevent the agreement from being delayed over that issue.

The bank will continue to administer the first, $1.4 billion account set up by the agreement. That money is to be used to pay bank loans made by American institutions to Iranian government borrowers during the shah's rule.

American bankers met in London last month with the head of Iran's central bank, Ali Reza Nobari, and presented him with a list of the outstanding amounts of loan principal and interest due them.

According to Iranian sources, Nobari took the list back to Tehran and is going over it with a committee made up of various government agencies. In the interim, the Iranians have asked that the period for negotiating settlement of these loans be extended an additional 30 days.