President Reagan sent a personal warning to Pakistan last month that a nuclear weapons development program there risks serious damage to U.S.-Pakistani relations, State Department sources said yesterday.

Reagan's Sept. 12 letter to President Mohammed Zia ul-Haq, as reported yesterday in The Wall Street Journal, spoke of "deep concern that this nuclear weapons issue could undermine all that we are trying to achieve."

Reagan evidently was referring to the $3.2 billion U.S. aid program, which was established in 1981. The Carter administration had suspended the earlier U.S. aid program in 1979 because of evidence that Pakistan was seeking to acquire a nuclear weapons capability through clandestine means.

Officials were reluctant to give details about Reagan's letter, but they described it as primarily concerned with reassuring Pakistan after increasing cross-border raids against Pakistani territory by Soviet-supplied aircraft from Afghanistan.

As part of this reassurance, the administration has offered to sell Pakistan early warning radar aircraft such as the Grumman E2C. Officials said discussions about such a deal are still in early stages.

State Department spokesman John Hughes, who declined to speak specifically of the Reagan letter, said the United States "on several occasions" had expressed concern to Pakistan about its nuclear program.

"As we have repeatedly stated, we have assurances from the Pakistan government that its nuclear program is entirely peaceful in intent and that it does not seek to acquire nuclear explosives of any kind," Hughes said.

The spokesman added that the administration believes the U.S. military aid program "may help remove the principal underlying incentive" for Pakistan to seek nuclear weapons by increasing its sense of security.

Conceding indirectly that Pakistan is still pursuing a worrisome nuclear program, Hughes said that "over time, we hope to persuade Pakistan that the pursuit of such a capability is neither necessary nor in its broader interests."