Gandhi was Indian prime minister when he was killed in May 1991 by a suicide bomber at a public meeting in the south Indian state of Tamil Nadu.
Pathmanathan, who became leader of the Liberation Tigers of Tamil Eelam (LTTE) in 2009, after their defeat by the Sri Lankan army, is also on Interpol's most wanted list on charges including arms smuggling and criminal conspiracy.
"The Court of Appeal issued an order to the Controller of Emigration and Immigration to prevent him leaving the country," said Sunil Watagala, a lawyer who had sought Pathmanathan's arrest
Pathmanathan had been the LTTE's chief arms procurer and run its global fund-raising network as it fought to carve out a separate state for minority Tamils in Sri Lanka.
Former president Mahinda Rajapaksa's government captured him in Southeast Asia in August 2009 and brought him to Sri Lanka. Pathmanathan then began cooperating with the government, and was released in 2012.
The coalition headed by Sri Lanka's new president, Maithripala Sirisena, pledged before his election victory last month to take legal action against Pathmanathan if it won.
Janatha Vimukthi Peramuna (JVP), a Marxist party that had backed Sirisena for president, then filed a petition seeking Pathmanathan's arrest.
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