The claims of the capture came as the Sri Lankan government insisted that the rebel Liberation Tigers of Tamil Eelam (LTTE) was close to being vanquished.
In an address to the parliament on Thursday, Ratnasiri Wickremanayake, the Sri Lankan prime minister, said: "Our forces have now surrounded the last stronghold of the terrorists. Our troops are challenging the Tigers waiting in front of their den."
Wickremanayake said that the government will only accept an unconditional surrender by the Tamil Tigers, who he said were "facing imminent defeat after a fruitless 25-year war for a separate Tamil homeland".
“The last moment of Tigers will be painful as well as decisive,” he said.
Disrupting rebel supplies
There was no immediate comment from the Tamil Tigers on the government claim, but the seizure of Chalai would disrupt rebel supplies as the sea base was used to receive arms and fuel from other countries through a widespread smuggling network.
Brigadier Udaya Nanayakkara, a Sri Lankan military spokesman, said the rebels still retained some capability to launch naval suicide missions from small bases along the coast.
"But for now, they are fighting a last-gasp battle for survival, bearing the brunt of a daily barrage of artillery," he added.
Sri Lankan troops have been engaged in an all-out offensive in recent months against the LTTE, which has been fighting since 1983 to carve out a separate homeland for ethnic Tamils in the country's north and east.
The United Nations and other aid agencies say some 250,000 civilians are trapped in the war zone.
As concerns grow for the trapped civilians, aid groups said that the last functioning hospital in the war zone was shut down down after being shelled for the fifth time in three days.
The International Committee of the Red Cross (ICRC) said staff and patients fled the hospital in Puthukudiyiruppu after an attack on Wednesday, the latest in a series that have left 12 people dead.
"We are shocked that a medical facility has again sustained direct hits. We have grave concerns for the well-being and safety of those who fled," Paul Castella, head of the ICRC's Colombo delegation, said in a statement.
The hospital's staff and 300 patients were evacuated to a coastal area deeper inside the war zone where there is no reliable source of drinking water, Sarasi Wijeratne, a spokeswoman for the ICRC, said.
Aid workers are trying to find them a better place to stay or get the military and the LTTE to grant them safe passage out of the conflict zone, she said.
Describing the plight of the fleeing patients, Sophie Romanens of the ICRC, said: "In the new place there was no adeguate medical facility to have more than 300 patients. So some of them are staying with family if they have relatives in that area.
"But most of them are in a community centre, which is just not a place to have so many patients.
"One of our colleagues described the scene inside the community centre; they said patients are lying on the ground with IV drips hanging from a tree."
Speaking to Al Jazeera on Thursday, Barbara Trachsel of the aid group Caritas, said: "From what we understand, the people are withheld in the territory by the LTTE.
"Most of these people also have their family with them, they are part of the peoplle being withheld.
"Our workers have not been able to leave the territory either, over the last few months."
The UN has, meanwhile, said cluster munitions appeared to have been dropped near the Puthukudiyiruppu hospital during the fighting.
Gordon Weiss, a UN spokesman, said 15 UN workers and 81 family members who were trapped near the hospital also fled after the area came under intense artillery fire, including what appeared to be cluster munitions.
Cluster munitions are controversial because of their ability to cause damage over a wide area.
Many of the so-called bomblets they contain do not explode immediately and pose a danger to civilians long after fighting ends.
Palitha Kohona, Sri Lanka's minister of foreign affairs, told Al Jazeera that "Sri Lankan forces have given categorical assurances that they are not using cluster bombs, nor are they procuring them".