Former army commander Sarath Fonseka had alleged that the military was behind some of the incidents in the north.
Jaffna Security Forces Commander Major General Mahinda Hathurusinghe however said that Fonseka was making baseless allegations.
The BBC Sinhala service quoted Fonseka as telling reporters outside court last week that the current security forces commander in Jaffna, Major General Hathurusinghe, was responsible for the spate of abductions and disappearance in Jaffna.
He also alleged that the Commander had taken money from the LTTE during the war when Fonseka was the Army Commander.
“The commander in Jaffna is the one who took Rs 30,000 a month as a bribe from the terrorist leader in Colombo during the war. He is the one who is behind these incidents” Fonseka was quoted by the BBC as saying.
Major General Hathurusinghe however told The Sunday Leader newspaper that another top ranking military officer had been charged for taking money from the LTTE and he was later presented in court and imprisoned.
He said that Fonseka was now making false statements over that incident and is going further by alleging that the army is involved in abductions.
Major General Hathurusinghe said that police records clearly indicate there were no “mass scale” abductions taking place in Jaffna and that the incident involving two JVP dissidents is being investigated.
“The army is assisting the police to investigate the incident regarding the two missing people. But that is an isolated incident. If you speak to the police you will find there are no abductions taking place on a daily basis as some claim,” Major General Hathurusinghe said.
JVP dissident group supporters Lalith Kumar Weeraraj and Kugan Muruganathan went missing in Jaffna on December 9 and have not been heard of since.