Lebanese Shi'ites say Libya kidnapped Imam Musa al-Sadr and two of his aides during a visit to the North African country in 1978. Libya says Sadr left the country safely. He is widely believed to have been killed shortly after he was seized.
"We decided ... to accuse Muammar Gaddafi... of inciting the kidnapping and withholding the freedom of... Imam Musa al-Sadr," said the court documents, approved by Investigative Judge Samih al-Haj late on Tuesday.
The charges, brought under Lebanon's terrorism law, carry the death penalty.
An initial case against Libya was closed in 1986 for lack of evidence. But Lebanon's public prosecutor said in August 2004 he would reopen the investigation after considering new evidence.
Sadr was the founder of the Shi'ite Amal Movement, from which the powerful Lebanese guerrilla movement Hezbollah later emerged.
He originally took up the plight of Lebanon's impoverished Shi'ite community before the 1975-90 Lebanese civil war. While Lebanon was dissolving into chaos, Sadr preached religious tolerance as he sought to organise the Shi'ites.
Sadr was born in Iran in 1928 and migrated to Lebanon. He remains a revered figure by all Lebanese Shi'ites.
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