Malik, a close aide of army chief Gen Ashfaq Parvez Kayani, had apologised to the court on October 22 and sought more time to hold the polls to over 40 cantonment boards.
Chief Justice Iftikhar Chaudhry, heading the bench hearing the matter, remarked that the court would not allow a delay in the elections in the name of changing legislation.
The apex court has directed authorities to hold the elections in cantonment boards on November 27 or December 7, news channels reported.
The court directed the federal government to decide on the matter within seven days.
Malik's counsel informed the apex court that an intra-court appeal had been filed against the indictment, to which the Chief Justice questioned if a decision had been made regarding the appeal.
The last elections to cantonment boards were held in 1998 and the bodies have been without public representation for 14 years, officials said.
While refusing to accept Malik's written apology at an earlier hearing, the chief justice said the responsibility for the delay in holding polls lies with the defence secretary.
On October 11, the apex court issued a notice to Malik, asking why action should not be taken against him under the contempt of court law for not holding the elections despite repeated instructions from the court.
The attorney general, the government's top law officer, too said that not holding the elections on time was a violation of the court's orders.
The Election Commission, in a letter sent to the government, has expressed its serious apprehensions over the delays in holding elections in cantonment areas.
Pawan Ruia's slipping turnaround tag
Look who does NOT want your opinion anymore
Let us solve our own problems, Pakistan PM tells US
The FIR against Birla that reignited a controversy
Cong's stand on opinion polls utterly puerile, blasts Modi