It has been alleged that Weeratunga is involved in arms sales to separatist rebels fighting troops in the Ukraine.
Foreign Minister Mangala Samaraweera has told an English weekly newspaper that the Ministry will conduct a full investigation into the matter.
Weeratunga has reportedly been involved with the sale of assault rifles and other small arms.
Weeratunga, a nephew of former president Mahinda Rajapaksa had been residing in the Ukrainian capital of Kiev and owns Club Lanka, a restaurant that served Sri Lankan dishes.
He was appointed Ambassador to the Russian Federation by former President Mahinda Rajapaksa. He served in Moscow for a record nine years until Minister Samaraweera recalled him together with all political appointees who were heading missions overseas.
However, Weeratunga did not return to Sri Lanka. His whereabouts are not known and he could not be contacted, the daily said.
During his tenure as the ambassador, Weeratunga was reportedly involved in a number of military procurements for Sri Lanka.