When President Reagan announced Wednesday's major shake-up of top arms-control officials, the name of Morton I. Abramowitz received only secondary billing.

But the choice of the veteran diplomat to be chief U.S. negotiator at the Mutual and Balanced Force Reduction talks in Vienna involves an issue of potentially crucial importance to the relationship between Secretary of State George P. Shultz and the career Foreign Service.

Within the service, what is known as the Abramowitz affair has been watched closely as a test of whether Shultz is willing to use his clout to protect career officers from the intrigues, whispering campaigns and purges that are the frequent byproducts of changes in administration.

For more than a year, the 22-year career of the former ambassador to Thailand had languished in the limbo into which he was cast when Shultz' predecessor, Alexander M. Haig Jr., tentatively chose him for the top Asia policy post of assistant secretary of state for East Asian and Pacific affairs.

Abramowitz never got the job. Nor did he get another post for which Haig subsequently tabbed him: ambassador to Indonesia.

In both cases, it later became known, the appointments were derailed by a shadowy campaign of opposition orchestrated by elements in the Pentagon and CIA, with the encouragement of congressional conservatives.

Stripped to its essentials, the case presented by his enemies was that Abramowitz, who had worked on several controversial policy issues during the Carter administration, was a man whose "political philosophy is akin to McGovern, Muskie and Mondale" and who thus should be regarded as suspect by the Reagan administration.

In the Foreign Service, what happened to Abramowitz has been viewed as a case of a professional officer conscientiously implementing the policies of an incumbent president and then, under a new president, being penalized for doing his duty.

The incident further lowered the morale of a service already concerned by what it views as the Reagan administration's excessive tendency to use diplomatic posts to reward its political cronies.

When Shultz took office last summer he found that he was being watched closely for signs of what he would do to right the injustice done to Abramowitz and to insulate the State Department bureaucracy from similar incidents.

One of Shultz' first moves was to ease out Richard T. Kennedy, undersecretary for management, who was widely regarded by professional officers as insensitive and inattentive to personnel problems, and replace him with Chicago businessman Jerome W. Van Gorkom, who has been charged with devising better work incentives for career officers.

But, these sources added, Shultz always was aware that if his efforts were to win credibility, he had to do something about Abramowitz.

As one source noted, "He wasn't about to make a futile gesture that would see him shatter his lance to no avail, but he was determined to correct the situation in a way that would send the appropriate signal."

Shultz had to navigate several mine fields. For one thing, there have been vague but persistent suggestions that anti-Semitism was a factor in the attacks on Abramowitz.

While department sources say it wasn't the primary consideration, they also say there is a message in the fact that Shultz chose another Jewish official, Paul Wolfowitz, for the assistant-secretary job that had been denied to Abramowitz.

Finally, there was the question of whether Shultz would be willing to risk a fight with the forces that had opposed Abramowitz earlier and to insist that the president back his move.

The tentative answer came Wednesday, when Reagan announced that Abramowitz would assume responsibility for the MBFR talks, which lately have been given renewed emphasis as part of Reagan's campaign to engage the Soviet Union in broad disarmament agreements.

For the Foreign Service, a more definitive answer will be available when Abramowitz goes before the Senate for confirmation.