The pilot's flying licence has been suspended pending investigation, a senior official of the Directorate General of Civil Aviation (DGCA) told PTI.
The two senior pilots have been grounded by Jet Airways since the incident.
Besides physically assaulting the woman commander, the pilot also left the cockpit unattended twice, which is in violation of the safety norms leading to the suspension of his licence, according to the official.
The aircraft was in the Iran-Pakistan airspace and was 2.45 hours away from its destination when the incident took place, an airline source told PTI.
When contacted, a Jet Airways spokesperson said there was a "misunderstanding" between the cockpit crew and the same was "resolved amicably" and "quickly".
"A misunderstanding occurred between the cockpit crew of 9W119 London-Mumbai flight on January 1. However, the same was quickly resolved amicably and the flight with 324 guests including two infants and 14 crew members completed its journey in Mumbai safely," the airline spokesperson said.
However, the source alleged that the male pilot who has been working with the airline for over a decade had some "argument" with the female commander over some issues.
The source said these two senior pilots have been flying together for many years and have had arguments in the past as well. But on Monday, arguments turned violent and the male pilot slapped the woman commander after which she came out of the cabin crying, the source alleged.
"The cabin crew persuaded her to go back to the cockpit but she refused. Following this, the male pilot came out of the cockpit, leaving the operations to the care of a cabin crew (which is a violation of flight safety norms) and persuaded her to return to the cockpit," the source said.
The airline has reported the matter to the DGCA and the pilots involved in the incident have been taken off duty pending investigation, the airline spokesperson said.