NCP chief Sharad Pawar will hold consultations with senior party colleagues to decide the future course of action.
Prime Minister Manmohan Singh and Congress chief Sonia Gandhi had sought to persuade Pawar not to press further for the resignation and held his party as a "valued" ally.
All India Congress Committee has also expressed confidence that the issues would be resolved. Last week, the NCP decided to pull out of the UPA government and support it from outside in protest against the way the party was treated by the Congress.
Pawar and the only other representative in the Union cabinet Praful Patel have informed the PM that they are tendering their resignation.
In a separate communication to Gandhi, Pawar has said the NCP, which has nine members in the Lok Sabha and seven in the Rajya Sabha, will stay part of the UPA.