The minister appears to feel that some prefects and police have been overzealous in applying their mandate to tackle threats to public order through searches of premises and house arrests.
"As a first choice and insofar as is possible, voluntary opening of doors should be sought," he writes, adding that searches must be "necessary and justified".
"Objective elements" must show that there are "serious reasons to believe that the place is frequented by a person whose behaviour threatens public order or security", the circular says, and "the name of the person and evidence linking him to the place" should be available.
Several cases of police breaking down doors without seeking permission to enter have been reported, for example at the Pepper Grill restaurant in Saint-Ouen-l'Aumône near Paris.
The owner's name was not cited in the warrant, which simply cited "serious reasons to believe that persons, arms or objects linked to activities of a terrorist nature" would be found.
If no crime is known to have taken place, police "have no powers of restraint", the circular reminds them, following reports that ecologist and libertarian activists have been handcuffed in controversial raids on people suspected of wanting to breach the ban on demonstrations introduced after the Paris attacks.
Some Green Party MPs and NGOs have accused police of exceeding their mandate to fight terror plots over the last few days.
In a case reported on the website of L'Obs magazine, police are alleged to have broken into the home of a young couple in the Barbès district of Paris using abusive language and handcuffing and beating the man because he had shouted at them not to hit another man they were arresting.
Both were detained for several hours and the man has been charged with assaulting a police officer, the site says, adding that police claimed they had heard the couple use the term "Daesh", a nickame for the Islamic State armed group.
Two appeals against house arrest were rejected by a Paris court on Friday.
One of the people involved asserted that no proof was provided of the serious offences alleged and that the detention had resulted in loss of employment.
But the judge accepted the authorities' argument that he had been involved with jihadi networks in Iraq 10 years ago, been in contact with several memers of a radical Islamist movement in 2014, given logistic support to Islamist prisoners under cover of helping their wives and recruited fighters in prisons.
By Friday 1,836 premises had been searched, 305 people had been placed under house arrest, over 200 people had been detained after raids and 293 weapons had been seized since the declaration of the state of emergency, Prime Minister Manuel Valls said during a visit to a town in the Paris region.