President Reagan gave his special commission on Central America its marching orders yesterday and expressed the hope that its pursuit of a long-range policy for the region will lead to closer U.S. ties with all of Latin America.

"I began this before I even took office," he said at an impromptu news conference, "to see if we can't make the borders meeting places instead of lines for confrontation or separation."

Reagan said he had told the commission, "I just hope we can bring this about and bring together the more than 600 million people in our two continents and the isthmus of Central America , and that their job would be to start with Central America."

The president met privately for half an hour with the 12-member commission, which is headed by former secretary of state Henry A. Kissinger. While being photographed with the group, Reagan said he was not worried that its report next February could be critical of administration policies.

"Not at all. We wanted a completely independent commission to find out something for a long-range policy, and they're going to remain independent," the president said. He sat between Kissinger and AFL-CIO President Lane Kirkland at a table that bore several jars of jellybeans.

In linking the commission to U.S. policy throughout Latin America, Reagan, on the eve of a trip to Mexico, seemed to be broadening the "North American accord" theme he first raised on launching his campaign in 1979, when he spoke of tightening bonds between Canada, Mexico and the United States.

Now, Reagan said, he wants to "bring all the nations of the Americas closer together" and "to alleviate some of the conditions that have made many of those countries subject to recurring revolutions, because the revolutions . . . for the most part have simply changed one set of rulers for another set of rulers."

Sen. Charles McC. Mathias Jr. (R-Md.), one of eight members of Congress named to advise the commission, told reporters on leaving the session that the president's views eventually could mean increased aid proposals for the region.

"It may be possible to develop a program which will cost something and which will have full administration support because of the way in which it's been conceived and developed," Mathias said.

Earlier, White House spokesman Larry Speakes went out of his way to emphasize that the continuing presence of dissenters in the group "flies right in the face of the knee-jerk reaction" by some administration critics that the commission was going to be "a rubber stamp" of approval for the Reagan line.

San Antonio Mayor Henry Cisneros, 36, a commission member who has criticized administration action in Central America, said as he left the gathering yesterday that he continues to have problems with the president's short-range policies.

He added, however, that the president had presented "a deep and moving statement about the poverty in the region" and had told the group, "that is the root cause of most of what we're dealing with as the result of hundreds of years of history, and we need to be speaking to that issue."

Speakes said the appointments of Cisneros, former Democratic National Committee chairman Robert S. Strauss and Yale economics Prof. Carlos Diaz-Alejandro were evidence that Reagan sought an independent commission.

"He wanted people with strong views and we have those people," Speakes said.

Diaz-Alejandro earlier drew fire from Sen. Paula Hawkins (R-Fla.) as being too sympathetic to Cuban President Fidel Castro. She sought unsuccessfully to have him removed.

Reagan defended the professor in his news conference, saying that, although routine security clearances for several commission members remain to be completed, "I think it is a fine commission and represents a variety of viewpoints and I hope that it will be passed intact."

He also repeated that the war games in Central America, involving 4,000 U.S. troops in Honduras and several warships off the coasts of Nicaragua, are essentially routine. He disputed allegations that the size of the games makes them different, saying that about 10,000 troops were involved in maneuvers in Panama in February.

A Defense Department spokesman, however, said there were 3,000 U.S. troops and 7,000 Panamanians in that exercise.