Pune based clubs Pune FC and Bharat FC had already decided to stop playing in the top division league earlier this year.
"It is correct that we have decided to pull out of the upcoming I-League season. We have notified this to the AIFF," Wahingdoh Secretary Anoop de Melo told PTI without elaborating.
Wahingdoh plied their trade in the I-League for the very first time last season and finished third on the standings under the guidance of Santosh Kashyap.
Pune FC and Bharat FC had failed to fulfill the financial and personal criteria according to the AFC as well as national regulations.
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Last year, the I-League was played among 11 teams and out of those, eight teams remain with the pulling out of three clubs -- Pune FC, Bharat FC and Royal Wahingdoh. With new entrants DSK-Shivajians, the I-League 2015-16 could be competed among nine clubs.
The 2015-16 I-League is expected in start in January next year after the end of the ongoing Indian Super League on December 20.