The federal anti-terror agency had asked Zeliang to be present for the questioning at its headquarters here today.
Zeliang has expressed inability to appear before the NIA, they said, adding that the agency will issue fresh summons to him.
The NIA is investigating massive scam in which funds meant for the Nagaland government allegedly went to militant group NSCN(Khaplang) and other regional terrorist organisations, according to the agency officials.
Zeliang was Nagaland chief minister during May 24, 2014 and February 19, 2017, and between July 19, 2017 and March 7, 2018.
Neiphiu Rio has become a new chief minister of the state and took over the office on Thursday.
Zeliang, leader of the Nagaland People's Front (NPF), is at present the Leader of Opposition.
A statement issued by his office has termed the timing of the summons as "conspicuously odd" and alleged political motivation and vendetta behind the move.
The NIA notice was served through a fax number belonging to the Chief Minister's Office, 15 minutes past midnight on March 12, after which a second letter was again served through the same number at 10:05 am the same day. The content of both the notices was similar, the statement said.
"In this regard, Zeliang has written to the NIA expressing his inability to appear at such a short notice and more importantly because of the Assembly session where he is required to attend as the Leader of Opposition," the statement said.
The NIA has been investigating extortion cases in Nagaland since August 2016 and Zeliang, as a law abiding Citizen of the Country, is ready to co-operate with any investigating agency, it said.
Earlier, on February 15 and 16, just before the state Assembly elections, the NIA had summoned for questioning three officials to Guwahati which included the OSD, media officer and public relations officer to the then Chief Minister, Zeliang.
On March 1, just before the election results were announced, an officer of Zeliang was again summoned and interrogated for five days, from March 3 to 7 at its Delhi headquarters.
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