However, it would have no effect on government formation as the NDPP-BJP combine has 30 MLAs, besides the support of two others, in the 60-member House. The NPP has two MLAs.
Nagaland NPP president Ato Yepthomi had submitted the letter of support in favour of the NDPP-BJP alliance to Governor P B Acharya Tuesday.
The governor had then asked Mr Yepthomi to give a letter of support signed by the party's national president, Conrad Sangma, along with a letter with the signatures of the two NPP MLAs, at the earliest.
However, Mr Yepthomi wrote to Mr Acharya this evening, saying he was yet to obtain the authorisation from Sangma and that was why he was withdrawing the letter of support submitted Tuesday.
"The reason for the withdrawal of the 'Letter of Support' is that we are yet to obtain the endorsement for the same from our national president," Mr Yepthomi wrote in the letter.
The NDPP-BJP alliance had won 30 seats (NDPP 18, BJP 12) in the February 27 Nagaland Assembly polls. The lone JD(U) MLA and an Independent have also extended their support to the alliance.
The NPP had contested the Assembly election in alliance with the Naga People's Front (NPF), but after the declaration of the results on March 3, it had decided to support the NDPP-BJP alliance.
The NPF had won 26 seats in the election.