The State Department official in charge of African policy conceded yesterday that the United States has fallen behind its original target date for a Namibia independence agreement. But he insisted that "the administration sees no reason to shift course."

Chester A. Crocker, assistant secretary for African affairs, stuck to that position in the face of largely skeptical questioning during testimony before the House African affairs subcommittee about the Reagan administration's efforts to induce South Africa to relinquish control over the predominantly black territory on its northwest border.

The administration, which has tried to improve relations with South Africa's minority white government, had hoped to start implementing an independence agreement by the end of 1982. However, the complex negotiations have bogged down, largely because of South Africa's insistence that there be a parallel agreement on withdrawing Cuban forces from the neighboring Marxist state of Angola.

At yesterday's session, Rep. Howard Wolpe (D-Mich.), the subcommittee chairman, and Rep. William H. Gray III (D-Pa.), representing the Congressional Black Caucus, charged that the administration's interest in linking the Namibia and Angola issues is enabling South Africa to stall on independence and increase its domestic repression of blacks, while alienating black Africa from the United States.

"The South Africans, whose concurrence and cooperation must be secured for any agreement leading to Namibian independence, have repeatedly made clear that they regard the Cuban troop issue as fundamental to their security concerns," Crocker responded. He argued that it is not realistic to expect progress if South Africa's fears of a communist military presence on its borders are not alleviated.

Acknowledging that the administration also would like to see the Cubans leave as part of a general settlement in southern Africa, Crocker quoted Vice President Bush, who said on a recent Africa trip that the United States "is not ashamed to state its interest in seeing an end to the presence of Cuban forces in Angola."

Crocker, who has had extensive talks with Angolan Foreign Minister Paulo Jorge about an Angolan withdrawal, said, "We believe important progress has been made, but there is still a long way to go....There is reason for hope."

If an agreement can be reached on parallel withdrawals of Cubans from Angola and South African forces from Namibia, he said, the administration believes other problems "can be wrapped up quickly."

But, in the face of repeated assertions by committee members that the administration should abandon the linkage and take a tougher line with South Africa, Crocker made clear that it will not shift its policy.

"Security, of which the Cuban troop issue is an integral part, has always been a prerequisite for agreement on Namibian independence," he said. "As a practical diplomatic matter, it will not be possible to obtain a Namibian independence agreement without satisfactory regional security assurances."

He added, "Quite apart from the diplomatic problem, it would not be desirable to bring Namibia to independence in circumstances that held the prospects for greater regional instability and turmoil. This administration would not be a party to it, and I would hope that no one in this room would wish to see that, either."

Asked to assess the prospects for an independence agreement, he said: "I would say that we are neither optimistic nor pessimistic. Instead, we have a realistic objective, and we are determined to move steadily toward it."