A drug-affected deckhand set off a flare causing a fishing boat to catch fire and sparked an expensive search operation off the Top End coast, a court has heard.

David Lawrence Morrison, 34, appeared in the Northern Territory Supreme Court on Friday for sentencing on four charges, including one count of aggravated assault and one count of damaging a vessel.

The court heard Morrison was working as a deckhand on a boat in July 2014 when he bought 1 gram of methamphetamine in Darwin before returning to the vessel.

Morrison injected himself with the drug and passed out in his cabin, before becoming dazed and going into a drug-induced psychosis.

The court heard he started hallucinating on the boat and demanded to get off the vessel, before threatening crew members with a knife and saying he would kill himself.

Morrison took the 25 centimetre knife and cut his left forearm, Justice Peter Barr said.

The crew hid the remaining knives on the boat but Morrison told the staff he could still "hit them with hammers".

Meth-affected fisherman tied up by crew

The court heard Morrison, who had been demanding a helicopter come and retrieve him from the boat, activated an emergency distress beacon, sparking a search operation at a cost of $13,372.

He also threw an Emergency Position Indicating Radio Beacon (EPIRB) overboard.

Justice Barr said Morrison threatened to shoot emergency flares into the boat's fuel tanks.

The court heard Morrison discharged one of the flares inside the wheel house, hitting a crew member and setting the boat's computer and navigations systems on fire.

The blaze was extinguished but caused more than $6,000 damage to the boat's electrical systems.

The crew restrained the man and tied him up as the boat made its way to Gove, where Morrison was taken into custody.

Morrison came to Darwin to 'break drug habit'

Justice Barr said it was accepted that Morrison had a psychotic response to the drug.

His medical records showed he had experienced multiple psychotic breakdowns induced by drugs in the past, the court heard.

The court heard Morrison "felt like a complete idiot" and was angry with himself over the incident.

The Canberra-born man had come to Darwin to break away from a drug habit.

In sentencing Justice Barr took into account Morrison’s pleas of guilty.

He was sentenced to three months' jail for the aggravated assault, 14 months' prison for threatening to use flares, and three years for damaging the boat.

His non-parole period is one year and nine months, and the sentence was backdated to July 2014.