In the wake of allegations from the air traffic controllers' union that the nation's airspace is unsafe, the Federal Aviation Administration has asked an independent group of airline organizations and pilots to evaluate air traffic safety.

The Flight Safety Foundation, a 400-member nonprofit international group promoting air safety, is to interview controllers and supervisors and examine "safety-critical equipment" and its maintenance and report to the FAA within 90 days, Transportation Secretary Drew Lewis said yesterday.

The National Transportation Safety Board, which also monitors air safety, yesterday voted unanimously to begin its own eight-week investigation to see whether doubts about air safety are justified.

Lewis noted that the NTSB is fundamentally a national organization and said that "because of the questions raised internationally," it seemed appropriate to have the foundation's evaluation also.

Meanwhile, Portuguese controllers ended their 48-hour boycott of flights to and from the United States at 8 p.m. (EDT). The boycott caused delays yesterday, and about 20 transatlantic flights were rerouted through Canadian airspace, an FAA spokesman said.

Controllers from Portugal, Spain, Italy and France are to meet Friday to draft a global boycott proposal, which they plan to present to the International Federation of Air Traffic Controllers Saturday.

Last week, the federation asked its 61 member associations to refrain from sympathy actions and urged President Reagan to negotiate with the Professional Air Traffic Controllers Organization.

On Monday, PATCO released a list of alleged incidents, including nine unconfirmed near-misses and other instances of planes flying too close to each other.

Internal memos from the Air Line Pilots Association also expressed concern about air safety, including worries that increased private plane traffic is producing "a definite safety hazard."

Last weekend, the FAA agreed to lift instrument flight-plan restrictions that occasionally were imposed on aircraft weighing less than 12,500 pounds at takeoff.

This will enable more regular flights by the 20 percent of the nation's 210,000 small planes that fly by instruments rather than visual flight rules, a spokesman for Aircraft Owners and Pilots Association said yesterday. The FAA agreement also called for more small-craft flights during off-peak hours.

Lewis said that all reports of near-misses are being investigated, adding that similar allegations by PATCO have been exaggerations.

Five near-misses were reported to the FAA during the first 12 days of the strike. During a 12-day period in August last year, there were 16 such reports, the FAA said.

Meanwhile, although at least 1,000 air controllers have sent form letters appealing their firing to the FAA, the Office of Management and Budget has received applications from 45,042 persons willing to replace them, FAA Administrator J. Lynn Helms said.

Another 130 controllers have asked to return, claiming they were intimidated into honoring picket lines, Helms said. The administration has agreed to review such cases.

Lewis said an independent task force will study "all 'people aspects' of the air traffic control system," including employment conditions, promotion and retirement.

"We recognize we have a problem that has to be addressed" concerning the controllers' needs, Lewis said, adding the problem probably had been "festering six, eight, 10 years."

The task force includes Lawrence M. Jones, president of The Coleman Co., Inc., which produces camping equipment; David G. Bowers, an associate professor of psychology at the University of Michigan, and Stephen H. Fuller, a vice president of General Motors Corp.

Lewis said he expects the task force to interview fired controllers as well as those still working.

In San Jose, Calif., yesterday, investigators said a controller warned one pilot that another small plane was nearby seconds before the two collided over the city library, killing one person Monday. They said the controller did his job properly.