The Federal Trade Commission, which ran out of money March 15, won a temporary new lease on life yesterday as both houses of Congress agreed to give the controversial agency $9.8 million to continue routine operations for 45 days.

The temporary funding was approved 216 to 201 by the House and 79 to 13 by the Senate.

The stopgap appropriation was designed to give House and Senate conferees time to resolve different approaches taken by the two houses in legislation to curb the agency's regulatory powers.

The conferees met briefly yesterday for a second time, resolving some fairly noncontroversial differences but failing to agree on the leading issues, such as the House demand for a one-house veto of FTC rules.

Congress has reached its budget ceiling for 1980 and cannot increase spending until it amends its budget resolution for the current year later this spring. So Congress got the money for the FTC by borrowing from funds approved earlier for the International Communications Agency, which includes Voice of America.

In the House, this prompted complaints by FTC critics that the money-shuffling would jeopardize VOA broadcasts to Iran and other Islamic countries -- a charge that was labeled "nonsense" by sponsors of the proposal, who said the ICA's operations would not be impeded.

Regular funding for the FTC has been held up three years because of the dispute over the agency's powers, forcing it to live off temporary appropriations, the latest of which ran out March 15. The agency was pushing for the new funding by the end of this week to avoid having to shortchange its 1,700 employes in their March 31 paycheck.

The conferees agreed to modify the agency's public participation program by limiting compensation to any one group to $50,000 annually or $75,000 for a single rule-making proceeding. They also agreed to devote 25 percent of the program's funds to small businesses.