Justice Minister Anisul Huq rejected widespread speculation linking S K Sinha's absence to the ruling, saying the top judge's decision was due to illness.
"He was formerly a cancer patient," Huq said, adding that those behind the claims "have mental problems" or "ill motives".
The head of Bangladesh's top bar association said Sinha was forced to take leave after he led the Supreme Court when it scrapped parliament's power to sack top judges.
"You know, the nation knows and the people of the world know a political party (and) the government have piled pressure on him in many ways," he said.
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"We think he was sent on a one-month leave as part of this pressure. He did not take the leave ... He was forced to."
Sinha made headlines in August when the Supreme Court scrapped parliament's power to sack top judges, in a landmark verdict seen as bolstering judicial independence.
The ruling was hailed by lawyers as a crucial safeguard for a secular judiciary in the Muslim-majority nation.
Lawyers said that without the provision, top judges would have been "subservient" to the government.
Prime Minister Sheikh Hasina brought the constitutional change allowing parliament -- controlled by her Awami League party -- to remove top judges in 2014.
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