The rebuke late Monday underscored how far Khan's relations have deteriorated with the powerful military, which backed his rise to power in 2018 but withdrew its support ahead of a parliamentary vote of no confidence that ousted him last year.
Pakistan is deeply mired in an economic and political crisis, with Khan pressuring the struggling coalition government for early elections.
At a weekend rally in Lahore, Khan repeated claims that a senior intelligence officer Major-General Faisal Naseer was involved in an assassination attempt last year during which he was shot in the leg.
The military's Inter-Services Public Relations (ISPR) wing said in a statement that "this fabricated and malicious allegation is extremely unfortunate, deplorable and unacceptable".
"This has been a consistent pattern for the last year wherein military and intelligence agencies officials are targeted with insinuations and sensational propaganda for the furtherance of political objectives," it said.
Criticism of the military establishment is rare in Pakistan, where army chiefs hold significant influence over domestic politics and foreign policy and have long been accused of interfering in the rise and fall of governments.
Prime Minister Shehbaz Sharif -- whom Khan also alleged was involved in the assassination plot -- weighed in on Twitter.
"His levelling of allegations without any proof against Gen Faisal Naseer and officers of our Intelligence Agency cannot be allowed and will not be tolerated," he said.
- Rejects findings -
Pakistan's government has said the assassination attempt was the work of a lone gunman, who is now in custody and who confessed in a video controversially leaked to media.
Khan rejects those findings and insists authorities have refused to accept his attempts to file a so-called first information report (FIR) with police identifying the real culprits.
Khan repeated his allegations in a video statement released Tuesday, saying that "there is no reason for me to fabricate the facts".
ISPR said it reserved the right to "take legal course of action against patently false and malafide statements and propaganda".
Khan faces dozens of charges that were brought against him since he was ousted -- a tactic analysts say successive Pakistan governments have used to silence their opponents.
He is due in court again on Tuesday.
Pakistan's military, the world's sixth largest, holds undue influence over the nation.
It staged at least three coups since the country gained independence in 1947 and ruled for more than three decades.
Ahead of general elections in October, a myriad of petitions and appeals are pending before the courts for an earlier vote for some provincial assemblies, which are usually held at the same time.
Pakistan's economy has also been pushed to the brink of collapse by years of financial mismanagement, exacerbated by a global energy crisis and devastating floods that submerged a third of the country in 2022.
The government is battling to revive the next tranche of a $6.5 billion loan deal agreed with the International Monetary Fund in 2019.
The IMF is demanding more stringent reforms, including tax rises and subsidy cuts, likely to rile voters ahead of an election.
Pakistan must also win guarantees of bilateral support from friendly nations to unlock the tranche, with China, Saudi Arabia and the United Arab Emirates already pledging loans.
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