Confirming the arrests today, Additional Director General of Police (CID), M R Krishna said all the documents used for making the bogus passport have also been found to be fake.
The accused was killed in an encounter with the Ahmedabad police in 2002 and was identified as Sameer alias Nawab Pathan from the passport recovered from his pocket.
Since the passport was made in Bhopal, the matter was handed over to the CID in Bhopal.
During investigations, it was found that one Subhash Sharma, a resident of Shajapur and passport agent Abu Bakerhad helped in making the bogus passport, following which the two were arrested yesterday.
Madhya Pradesh Home Minister Uma Shankar Gupta said the matter was being probed further and added that action will be taken against those found guilty.
A group of militants allegedly belonging to banned Lashkar-e-Taiba had attacked the temple in Ahmedabad on September 24, 2002, killing 37 people and leaving scores others injured.