President Reagan yesterday removed Thomas O. Enders as assistant secretary of state for inter-American affairs, an action that reflected "unhappiness with the execution of U.S. policy" in Central America, according to an administration official.

Several administration officials said the change will lead to a tougher U.S. policy in Central America, controlled directly by the White House rather than through the State Department.

Enders will be replaced by Langhorne A. (Tony) Motley, a land developer and Republican Party stalwart from Alaska who has been ambassador to Brazil for the last two years.

The official who spoke of Reagan's "unhappiness" also praised Enders' diplomatic abilities, which he said would be put to proper use in his new post as ambassador to Spain. But, in a sharp implied criticism of the way Enders had performed his present duties, he added, "You don't handle Central American policies with tea and crumpets on the diplomatic circuit."

Several administration officials said U.S. policy in Central America now seems likely to increasingly bear the stamp of Reagan's national security affairs adviser, William P. Clark. He is sympathetic to the view, shared by U.N. Ambassador Jeane J. Kirkpatrick, that even tougher measures are required to combat leftist guerrillas in El Salvador and to counter the influence of Cuba and and the leftist Sandinista government of Nicaragua in that region.

They regarded Enders as favoring a diplomatic solution to the civil war in El Salvador. Reagan agrees with Clark and Kirkpatrick that the guerrillas must be defeated militarily, the officials said.

One official added that Reagan decided to "put his own people" into key Central America policy-making positions even before he made his speech on Central America to a joint session of Congress on April 27.

However, other sources in the administration cautioned that it would be incorrect to assume there will be swift and radical changes in Central American policy, which is under heavy fire from liberals in Congress. In particular, these sources disputed the idea that Enders' departure means that Clark has wrested control of the policy from Secretary of State George P. Shultz.

Shultz, who announced the change yesterday to reporters aboard Air Force One en route to the Williamsburg, Va., economic summit, praised Enders as "a great man" and said the move was made because it was time for a "rotation in the State Department, and we do make changes."

The extent of Shultz's involvement in the decision was not clear, but one official said that the secretary "fully concurred" in the switch. This suggested that Shultz did not initiate the move. But he was said to be pleased with the elevation of Motley, who has been given almost universally high marks as ambassador in Brazil.

On the surface, Enders' replacement would seem to be a relatively unremarkable move, as his job is nominally a second-echelon position in the governmental hierarchy. However, it seems certain to stir controversy because U.S. involvement in Central America is a subject of emotional national interest and Enders has been regarded as the principal architect of U.S. policy in the region.

In the view of many officials, Enders' problem was that he had come to exercise a power over Central American policy decisions far greater than is normally granted to assistant secretaries of state. That was particularly the case after Shultz took office last summer and found himself forced to devote most of his time to the Middle East and other problems.

In the process, Enders became, as one source put it, "a man caught in the middle. Although he got on well with Congress, he still was pushing a policy fiercely opposed by liberals fearful of increasing U.S. involvement. At the same time, his efforts to build support with the liberals made him highly suspect to hard-core conservatives who thought him insufficiently vigorous in his anti-communism."

As the civil war in El Salvador dragged on inconclusively, Enders also found himself increasingly on a different wavelength than Clark, Kirkpatrick and other in-house critics from the Pentagon and the CIA who disputed the State Department's approach.

As one senior official put it, "It was like what happens when a baseball team is on a losing streak. You get a lot of agitation to fire the manager, and Enders was regarded throughout the government as the manager on Central America."

Clark and Kirkpatrick's disenchantment came to a head in February when it became known that Enders had prepared a position paper advocating a two-track policy of pursuing the civil war in El Salvador while seeking to promote negotiations with representatives of the guerrillas. This was opposed by administration hard-liners as potentially opening the way for the guerrillas to negotiate a share of power in the Salvadoran government.

The uproar caused by that incident in conservative circles forced Shultz to exercise greater supervision over Enders' activities. But by then the demand for Enders' ouster had become a crusade for conservative Reagan supporters.

At the same time, the president began to turn increasingly to Clark and Kirkpatrick for advice on Central America. The sugar import quota for Nicaragua was virtually eliminated despite Enders' objections. He was unable to fill the key deputy slots in his bureau because of a power struggle over the ideological orientation of those considered for the jobs. And, in what was widely regarded as a slap at Enders, former Florida senator Richard B. Stone was named a special emissary for Central America.

Enders' replacement, Motley, is held in high regard by Republican conservatives. And, although he went to Brazil two years ago with the reputation of "a real estate salesman from Alaska," he has won considerable praise from Brazilian officials and other diplomats for skillful performance.

Motley, who was born and raised in Rio de Janeiro, speaks Portuguese. He arranged Reagan's visit to Brazil last December and acted as his interpreter in meetings with Brazilian President Joao Figueiredo.

However, Motley's Latin American experience has been confined largely to Brazil. State Department officials said he has no real experience with Central America.