The Federal Election Commission yesterday refused to certify formally to the Treasury Department that independent presidential candidate John B. Anderson would, under certain circumstances, be eligible for a government reimbursement for some of his campaign expenses.

Although the commission advised Anderson last week that he would be eligible for federal funds after the Nov. 4 election if he gets at least 5 percent of the vote and meets other requirments, the regulatory agency said it would be premature to issue a formal certification at this time.

Anderson still is expected to collect some money from the government after the election if he does well at the polls. The main impact of yesterday's FEC decision is expected to be on Anderson's ability to borrow money immediately, using the reimbursement as a sort of collateral.

An effort is under way to borrow $10 million from banks in Chicago and New York and on the West Coast, Anderson aides have acknowledged.

In its decision yesterday, the commission said ultimate eligibility will depend on whether Anderson actually gets 5 percent of the presidential vote on election day.

"In that the 1980 presidential election has not taken place, the commission cannot determine at this time whether Congressman Anderson has met the condition of [funding eligibility under the law] nor the amounts to which Congressman Anderson would be entitled of the Treasury for payment . . . if such condition of eligility is met," the FEC said adding:

"Therefore, even if Congressman Anderson has met the eligibility requirements, certification of the congressman would be premature."