Sangma is the declared candidate of Tamil Nadu Chief Minister J Jayalalithaa and her Orissa counterpart Naveen Patnaik.
He is being seen as a likely NDA candidate as well, against ruling UPA’s Pranab Mukherjee.
The NDA however is yet to take a decision in this regard.
Sangama’s resignation was announced by Janata Party President Subramanyam Swamy who met Sangama on Wednesday.
"I hereby tender my resignation from the primary membership of NCP with immediate effect. I place on record my deep gratitude to the President, other office bearers and rank and file of NCP for the courtesies extended to me by them at personal level while I was a member of the party," he wrote in his resignation letter.
In a statement, Sangma said he had "no option but to resign" from NCP "without any personal intent whatsoever of embarrassing the party and its leadership".
Talking about the circumstances in which he had to quit, the 64-year-old leader said, "disinclination of the NCP to endorse my candidature amounts to a denial of the aspirations of the tribals of the country."
He noted that his candidature had been projected by the Tribal Forum of India and he cannot "ignore the feeling of the tribals that Raisina Hill (Rashtrapati Bhavan) should not continue to be a distant dream for them."
NCP Chief Sharad Pawar has meanwhile said the party has accepted Sangma’s resignation.
NCP had opposed Sangma’s candidature and had also hinted at disciplinary action if he refused to toe the party line.
NCP office bearers are scheduled to meet on Thursday, to further discuss the issue of presidential polls.
Meanwhile, leader of Opposition in Lok Sabha, Sushma Swaraj, Janta Party President Subramanyam Swamy and BJP leader Jaswant Singh met at the residence of senior BJP leader LK Advani on Wednesday evening.
The meeting discussed the strategy to be adopted for the Presidential polls. The meeting discussed the strategy to be adopted for the Presidential polls.
NDA is likely to decide by Thursday on whom to support for the race to Raisina Hill.
Pranab is suitable candidate, says Yeddyurappa
Estranged BJP leader and former Karnataka Chief Minister BS Yeddyurappa said UPA nominee Pranab Mukherjee is a “suitable man” for the post of President, but the party central leadership would take an appropriate decision on the issue.
Left parties to meet tomorrow
Top leaders of Left parties will meet in New Delhi on Thursday to take a decision on the issue of supporting UPA Presidential candidate Pranab Mukherjee.
Prakash Karat, Sitaram Yechury and S Ramachandaran Pillai from CPI-M, A B Bardhan, Sudhakar Reddy and D Raja from CPI, Debabrata Biswas and G Deverajan from Forward Bloc and TJ Chandrachoodan from RSP will attend the meeting.