Thirteen other people died and 100 were wounded in the suicide bomb attack on Sunday.
Fernandopulle, the second Sri Lankan minister to die in an attack blamed on the LTTE this year, was part of a government team that held failed peace talks with the guerrilla group.
Sri Lanka pulled out of a six-year-old truce with the LTTE in January, leading to a sharp rise in fighting.
Sri Lankan government troops at
Nagarkovil, north of Colombo [EPA]
Helicopter gunships were also sent to attack LTTE bunkers in the northern peninsula of Jaffna on Monday, Sri Lanka's defence ministry said.
It also said 22 more LTTE fighters had been killed by Sri Lankan forces over the weekend.
The LTTE has been held responsible for about 240 suicide attacks in recent decades and is listed as a terror group by the US, European Union and India.
The group has fought since 1983 for an independent homeland for ethnic minority Tamils after decades of rule by governments run by the Sinhalese majority.
More than 70,000 people have so far died in the conflict.