"If there was a foreign conspiracy, would we be sitting silently? It would be a big sin," he said.
Bajwa said so far the military had showed restraint, but issued what appeared to be a veiled warning toward Khan, saying “keep it in mind that there is a limit to patience".
There was no immediate comment from Khan's party to the army chief's remarks. Pakistani President Arif Alvi has hosted at least one meeting in the capital of Islamabad between the former premier and Bajwa to attempt a reconciliation between them.
Earlier Wednesday, Sharif's office said on Twitter it had received a summary about the candidates for a new army chief from the Defense Ministry, which received the initial list of nominees. The military also tweeted it had nominated a list of six senior generals.
Khan has been pressuring Sharif to resign. The former cricket hero started a protest march from the eastern city of Lahore on Oct. 28 before surviving an assassination attempt this month that killed a by-stander and wounded 13 others.
Since then, Khan's protest march has moved toward Islamabad in convoys without him.
The bitter political feud between Sharif and Khan comes as Pakistan struggles to deal with the aftermath of last summer’s devastating floods. Thousands are still living in makeshift homes following the record-shattering floods that killed 1,739 people and affected 33 million.
So far, neither the military and nor the government has disclosed the names of the nominated generals for the top army post. Pakistan's six most senior generals are Lt. Gen. Asim Munir, Lt. Gen. Sahir Shamshad Mirza, Lt. Gen. Azhar Abbas, Lt. Gen. Nauman Mehmood, Lt. Gen. Faiz Hamid and Lt. Gen. Mohammad Amir.
Bajwa is retiring at a time when Khan is asking Sharif to announce snap elections, a demand that the coalition government has rejected, saying the next parliamentary vote will take place in 2023 as scheduled. Bajwa became army chief in 2016 and Khan extended his service for three years.
It is widely believed that Gen. Asim Munir, a former spymaster, is a top contender for the senior post. Sharif has the authority to pick any of the generals nominated by the military.