Gen. Abdul Razeq, a leading police commander, was killed, an aide said.
Investigators wearing white white suits and carrying boxes of evidence emerged from the building early on Thursday morning.
Penny, who resigned last year, was indicted last month on felony charges of tampering with evidence.
The man, who was described as alert and talking, was being flown to a hospital for treatment.
Authorities insist the case posed no risk to humans.