Justice Rajiv Sahai Endlaw said, "Just because PM is involved we cannot drag it on" and the Election Commission of India (ECI) being a constitutional body was "seized of the matter".
"Without going into the controversy raised in the writ petition, it is disposed of," the court said.
ECI, meanwhile, assured the court that it will take a decision within a reasonable period of time.
The commission also said that election results were declared on May 16, 2014, and the complaint against Modi was first received by it on June 2, 2015, more than a year later.
The petitioners, former Congress MP Rajesh Mishra and another leader Prajapati Nath, had in their plea sought a probe by ECI into their complaint as well as disqualification of Modi as an MP.
The plea, moved in the high court on August 2, had also alleged that the poll panel has been sitting on the complaint against Modi as he is the Prime Minister.
The plea had said that while Modi's poll expenses return filed with district electoral office, Varanasi, showed his total expenditure to be around Rs 37 lakh only, the actual figure was "far beyond prescribed maximum limit of Rs 70 lakh".
In their petition, the Congress leaders had contended that Modi was required to maintain and lodge true and correct statement of the account of his election expenditure.
"A perusal of the statement of election expenses filed by the returned candidate, reveals that he has failed to keep separate and correct account of all expenditure in connection with his election and has also not furnished true and correct statement of account of election expenditure, incurred by him in Varanasi Constituency as per law," it had said.
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