Spokesman Micky Rosenfeld told AFP a second rocket struck open ground.
A military spokesman said the building was a factory, and Rosenfeld said four workers were able to escape after the attack.
"Once the fire was extinguished, we began a search of the interior to determine whether there was anyone still there," he said.
The privately run Channel 10 television station said the building was a paint factory and that one employee was slightly injured and taken to hospital.
Rocket attacks from the coastal enclave yesterday were followed by more air raids overnight.
Of four early morning strikes on Gaza, two targeted "sites of terrorist activities" and the others hit arms depots and production facilities, a military spokesman said.
Palestinian medics said the air raids that killed the two men struck near the home of Ismail Haniya, the former Hamas premier who stepped down on June 2 when Gaza and the West Bank set up a unity government.
Prime Minister Benjamin Netanyahu has urged the international community to press Palestinian president Mahmud Abbas to end his reconciliation with Hamas, citing the alleged kidnapping as proof that the movement's "terrorist" activities make it an unsuitable political partner.
Five Palestinians have been killed in the Israeli security sweep to find the teenagers and more than 400 have been arrested, mostly Hamas members.
Troops have also raided some 2,100 buildings in the West Bank, a military spokesman said.
