he level of U.S. security assistance to Greece will depend in part on the current negotiations on the future of U.S. bases here, President Reagan has told Greek Prime Minister Andreas Papandreou.

This was the message in a letter, released here today, in which Reagan replied to Papandreou's Feb. 4 protest against U.S. plans to increase aid to Turkey but not to Greece for the next fiscal year.

Papandreou had argued that these plans would upset the standing balance of power between Greece and Turkey in the Aegean. Greek-Turkish relations are tense because of territorial disputes in the region. "In the eastern Mediterranean as elsewhere we seek to establish . . . a structure of peace that strengthens the ability of states in the region to deter aggression from without while promoting improved relations within the region," Reagan's letter stated. "In considering levels of security assistance to Greece my administration will continue to be guided by this objective."

But the Reagan letter reaffirmed the link between the Greek aid issue and the current U.S.-Greek talks on a new defense and economic cooperation agreement. "I regard a new agreement to define our security relationship to be in the interests of both our countries," Reagan wrote. "In this context, the administration will seek increased levels of security assistance for Greece above the levels of the current program."

There was no formal reaction by the Greek government to the Reagan letter today.