A chartered airliner filled with nearly $3 million worth of medical supplies is heading for the Soviet Union's three Baltic republics and the Ukraine, bypassing Moscow.

The shipment, which was leaving Wednesday, has political overtones because the supplies are being sent directly to the independence-minded Baltics instead of through the Soviet capital. Some press commentaries in Moscow have criticized the gesture as an infringement on Soviet national sovereignty.U.S. officials respond that the aid program is strictly humanitarian, pointing out that future shipments will be sent to other regions in the Soviet Union.

The Boeing 707 is due to arrive on Thursday in Latvia, where the cargo will be divided for shipment by truck to hospitals and health-care facilities in Latvia and the other two Baltic republics, Estonia and Lithuania.

The plane will fly the remainder of the cargo to the Ukraine for victims of the 1986 nuclear accident at Chernobyl.

The project is being funded partly by the U.S. Agency for International Development and by several pharmaceutical companies, which are donating the supplies.

AID is contributing $5 million for administrative costs, and officials hope donations from the drug companies will be in the $10 million-$15 million range in 1991.

The U.S. government is prohibited by law from funding development projects in communist countries unless there is a waiver. There is no ban on emergency humanitarian assistance, and this type of help was provided after the earthquake in Armenia in December 1988.