The provincial government media office in a statement confirmed the attack on the mosque in Mohammad Agha district.
The statement further added that a group of armed militants stormed into a mosque in Surkhabad area, leaving at least two prayer participants dead.
According to the provincial government, a tribal elder identified as Sher Agha Kochi was among those killed and two others were wounded.
In the meantime, the local officials in Mohammad Agha district said Kochi was a former commander of Hezb-e-Islami a local influential tribal elder.
No individual or group has so far claimed responsibility behind the attack.
Logar is among the relatively volatile provinces in central Afghanistan where the Taliban insurgents are actively operating in a number of its remote districts.
The group often conducts insurgency activities by placing landmines and carrying out coordinated attacks against the government and security forces.