The leading carrier has seen a series of top level exists in the last two-and-a-half years. Its Chief Executive Officer Cramer Ball had resigned in December 2015.
Nambiar, who had joined Jet Airways from Etihad in 2014, is said to be moving back to the Gulf carrier.
In a statement, Jet Airways said Nambiar has tendered his resignation.
"We thank him for his contribution to Jet Airways and wish him the best in his future endeavours," the airline said.
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Whole-time Director Guarang Shetty is serving as acting CEO after Cramer Ball's resignation. Ball became the fourth CEO of the private airline to quit since April 2013 when it offloaded a part stake to Abu Dhabi's national carrier Etihad.
Apart from Ball, two other senior executives had put in their papers last year. In September last, Jet Airways Vice President for Fleet Management Krishnan Balakrishnan had left the carrier to join budget airline GoAir as its Chief Financial Officer.
from Rs 20,966 crore in 2014-15 fiscal.
"Passengers carried increased by 14.8 per cent to 25.8 million in FY16 from 22.5 million in FY15... Code share traffic surged by 31 per cent from 1.6 million passengers carried in FY15 to 2.1 million passengers in FY16," the airline said.
Further, Jet Airways said that passengers and revenues delivered by Etihad Airways and Etihad Airways partners rose 86 per cent and 72 per cent, respectively in the last fiscal.
It also noted that cash generated from operations, after financing expenses, was primarily used to reduce debt by Rs 1,680 crore.
"... Etihad Airways is committed to its partnership with Jet Airways and is focused on driving further synergies, along with other Etihad Airways Partner airlines," Jet Airways Vice President James Hogan said.
Hogan is also the President and CEO of Etihad Aviation Group.
Goyal emphasised that customer satisfaction, network enhancement and driving benefits through further improvements in operational efficiencies would continue to be the carrier's key priorities.
"The competitive and structural challenges in the Indian aviation market continue to exist. In addition, the induction of capacity and the enhanced competitive scenario is creating a constant pressure on yields," he said.