An HC bench of Justice JBM Hassan and Justice Md Khairul Alam passed the order following a writ petition.
The Chief Judicial Magistrate of Satkhira has been asked to investigate the incident and submit a report within three months.
The court also issued a rule seeking explanation as to why directives should not be given to preserve the forest.
Sixteen people, including Environment, Forest and Climate Change, and Home secretaries, Inspector General of Police, Director General of Bangladesh Coast Guard, Satkhira Deputy Commissioner, Superintendent of Police and officer-in-charge of Shyamnagar Police Station, will have to respond to the rule within four weeks.
The incident of deer poaching came to light on July 9 when a media report said Coast Guard and Forest Department jointly recovered 20 slaughtered deer and six firearms from Sundarbans under Satkhira district and detained some members of police from the spot in this regard on July 8.
According to the report, the poachers also cooked and ate away two deer.
However, sub-inspector Liton of Shyamnagar Police Station who was among the detainees prevented the Forest Department officials from filing cases over the incident and instead he filed two cases accusing six people mentioning that three dead deer and three firearms were recovered.
Following the report, Abu Bakar, editor of weekly Naya Barta, filed the writ petition on July 25.
Shamsul Haque, lawyer of the petitioner, said SI Liton threatened to kill the Forest Department and Coast Guard members and tried to cover up the incident.