The complaint was filed by AICC legal cell Secretary K C Mittal on behalf of local party leaders Rajesh Mishra, a former MP, and city party chief Praja Nath Sharma.
Mittal said that a Congress delegation made a representation to the full Election Commission which assured it that it will look into the matter.
The complainants alleged that Modi "failed" to give "true and correct" account of election expenses to the EC and that he undertook an "opulent" campaign through a "swanky" election office.
The complainants also wanted all expenses incurred by RSS volunteers in Modi's campaign to be added in his poll expenses as "RSS is not a body registered as a Society or an association, nor as a registered political party and is not an official constituent of BJP".
Also Read
Congress also accused Modi of not submitting his travel expenses individually or along with other star campaigners.
"We request that the matter may be proceeded further and necessary action may be taken to disqualify him," they added.