The airline said it was forced to halt service between Dubai and Abu Dhabi and the Indian cities of New Delhi and Mumbai, a local news report said.
The sick-out by 361 of its 760 captains and first officers also affected flights to Qatar, Kuwait, Bahrain, Oman and Saudi Arabia, it said.
All passengers in the UAE stranded by the sick-out would be accommodated on flights of Emirates Airline and Air India, a Jet Airways official was quoted by Khaleej Times as saying.
About 13,000 passengers were affected, the airline said.
"The situation is very fluid right now but we are closely monitoring the situation and will do everything required to ensure minimum inconvenience to our customers," the airline said on Tuesday describing pilots' approach as a "simulated strike".
A total of 186 flights -- 154 domestic and 32 international -- had been cancelled or affected throughout its network, the airline said. The strike also grounded most of the carrier's domestic flights.
However, all of its wide-body aircraft on long-haul flights were operating normally, thanks to their foreign pilots, who apparently did not participate in the sick-out.
Asif to be deported soon: Reports
Ex-Bangladesh premier Hasina returns
UAE in contact with India over detained plane
Kolkata: UAE plane carrying arms detained
Haneef cancels Australian visa to cash in on PF