He made the claim when answering a question by reserved seat MP Selina Jahan Lita on Monday who asked whether the failure to find Pinak was administrative or technological.
"It's neither," Khan replied. "Rather it's a natural cause."
Local administration called off the search and rescue operations on Aug 11, eight days after the vessel sunk at Munshiganj's Mawa.
Rescuers recovered 48 bodies while the official figure put the number of missing at 61.
"The launch could not be recovered mainly because of turbulence in the river, strong current and whirlpool, large amount of silt carried by the current and rough weather," the minister said.
A 'metallic object' roughly the length of Pinak-6 was detected underwater but divers could not get to it.
According to him, 'extremely bad weather' was the biggest hindrance for the rescuers to reach the sunken vessel.
The reserved seat MP asked whether any initiative had been taken to remove silt from Padma.
Minister Khan said it was not possible due to strong current and added that steps would be taken to this end later.
The shipping minister revealed that various passenger ferry accidents over the past 38 years had killed 3,683 people in Bangladesh.
Replying to a question, he said the government had records of 558 accidents since 1976. A total of 450 people had remained untraced in these accidents.
He identified natural calamities, rough weather, vessel owners’ negligence, passenger ignorance, and unapproved vessels design as some of the reasons for river accidents.
Responding to another query, minister Khan said that Bangladesh currently had four rescue vessels.