"We are looking at the possibility of arson as well as an accidental fire," Rohana told AFP. "The fire started in the upper floor and we are still investigating."
The blaze came a day after Sri Lanka's Muslim minority shortened their Friday prayer services because of heightened religious tensions after clashes with hardline Buddhists earlier in the week in Kalutara district.
The district includes Panadura, and the popular and mainly Muslim coastal resorts of Alutgama and Beruwala, where religious riots earlier in the week killed four and wounded 80. Hundreds of homes and businesses were set on fire in the violence.
President Mahinda Rajapakse, who toured the riot-hit resort of Beruwala, said he was ordering a probe into "recent disturbances". "I will be appointing a high-level panel to inquire into recent disturbances," the President said on Twitter.
The president, who is a member of the Buddhist community, made no reference to the fire at No-Limit, but he had previously asked Buddhists and Muslims not to whip up extremism.
The Muslim Council of Sri Lanka said Islamic clerics instructed mosques to conduct shorter services and asked the faithful to disperse peacefully after lunchtime prayers on Friday.
Muslim-owned businesses shut down in Sri Lanka's capital Colombo on Thursday to protest against the riots by extremist Buddhists, defying Rajapakse's plea to stay open.Police said workers had carried out some electrical repair work at the No-Limit store the day before the blaze. There were six people at the store, including two unarmed guards at the time of the pre-dawn fire, he said.
Witnesses said they heard several explosions as the fire completely gutted the two-storey building.
Authorities tightened security in the area following the blaze.
In March last year, two Muslim-owned clothing stores, including No-Limit, came under attack from Buddhist mobs.
Muslims account for about 10 percent of the 20 million population in the mainly-Buddhist country.