The White House has decided to give a "recess appointment" to retired Army Gen. George M. Seignious, allowing him to begin working as director of the Arms Control and Disarmament Agency without Senate confirmation.

This decision - which may be announced today, according to informed sources - has provoked concern among some arms control activists who are unhappy with the prospect of a general running the government agency that is supposed to work for arms control.

Their concern typifies the delicate political problems the administration faces in trying to keep its natural allies in line while searching for new support for a strategic arms agreement with the Soviets.

Administration officials acknowledge privately that they sought out a military man to head th agency after the resignation of Paul C. Warnke in hopes of winning new friends for a SALT strategic arms limitation treaty among moderates in the country and in the Senate.

But the idea of a general running the agency strikes some ardent arms controllers as comparable to putting the fox into the chicken coop. One group, the Federation of American Scientists, has openly opposed a recess appointment for Seignious on the Senate Foreign Relations Committee from inquiring fully into the general's qualifications for the job.

Under a recess appointment Seignious could serve for up to a year, or until the Senate choose to act on his nomination.

The Federation of American Scientists' statement followed by several days a letter to President Carter from four leaders of pro-arms control groups complaining that the administration may be paying too high a price to win new friends at SALT.

Specifically, the letter opposed reported administration decisions to send Congress a supplementary military appropriations bill, to expand its civil defense program and to build some component parts of the so-called neutron bomb.

The letter said these measures were inconsistent with Carter's stated arms-control goals. It was signed by representatives of the Union of Concerned Scientists, the Council for a Livable World, the Committee for East-West Accord and New Directions.