Mel has already been in detention for six months.
"The court believes the restriction of the suspect's rights does not breach the principle of proportionality," the court said.
Mel, a former Soviet officer who served in Vilnius during the 13 January 1991 events, was detained at Panemunė border checkpoint on the Lithuanian-Russian border on March 12.
He faces life imprisonment on charges of war crimes and crimes against humanity.
Prosecutors maintain Mel was in one of the tanks that stormed the Vilnius TV tower in the early hours of 13 January 1991.
All in all, 79 citizens of Russia, Ukraine and Belarus are named suspects in the 13 January case, with European arrest warrants issued for their arrest.
Fourteen people were killed during an attempt by the Soviet army and special forces to take over the Vilnius TV Tower on 13 January 1991, and more than 1,000 unarmed civilians were injured.
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