Observers say the two sides are gearing up for major confrontation in the north.
A military statement said that the four aircraft had carried out a "successful air strike" on a bunker in Jayanthinagar in Kilinochchi.
"Intelligence had confirmed that the bunker complex was frequented by Mr Prabhakaran," the statement said.
Last month, an air force strike killed the rebels' political chief, SP Thamilselvan, who was at a meeting with other leaders at Kilinochchi.
Soon after, the government marked Prabhakaran's 53rd birthday with a vow to kill him.
Defence Secretary Gotabhaya Rajapaksa told the AFP news agency: "We are after him [Prabhakaran]. We are specifically targeting their leadership."
A Norwegian-brokered 2002 ceasefire broke down two years ago, resulting in renewed fighting that has killed more than 5,000 people.
At least 70,000 people have died since the war began in 1983.