The storm remains a Category 2 cyclone but is now about 30km southwest of Darwin and 30km east-northeast of Dundee Beach.
All flights due to arrive or depart from Darwin International Airport have been cancelled into tomrrow morning.
Shelters were opened across Darwin as the cyclone approached.
COOLALINGA EVACUATION
Emergency services were called out to a petrol station just before ten o’clock this morning to...
Posted by Northern Territory Police, Fire and Emergency Services on Friday, 16 March 2018
NT Emergency Services chief officer Jason Collins advised anyone not already in secure shelter to make their way there immediately.
"This is a dynamic situation, the conditions can and will change over the course of the event," he said.
"The eye will pass through, this is not over, you will get winds coming back and this will go into the late afternoon."
Marcus was rated a category 1 storm as it developed off the NT coast on Friday but was expected to intensify to category 2 as it crossed the Cobourg Peninsula.
It has sustained wind speeds near the centre of 85kmh, with gusts of up to 120kmh, the Bureau of Meteorology says.
Marcus is expected to move southwest across the Van Diemen Gulf during Saturday and may weaken as it crosses surrounding coastlines.
People have been warned to stay away from beaches and coastal areas, with higher than normal tides expected.
Heavy rains mean Darwin could receive around 200 millimetres over 24 hours, raising the possibility of localised flooding.
Yesterday Darwin supermarkets were selling out of water as Top Enders rushed to replenish their cyclone kit supplies.
Police had been in touch with organisers of St Patrick's Day events and asked them to cancel.
"Even if the event's not necessarily cancelled by the event organiser I'd suggest it's not the best idea to be travelling in this type of weather," Regional controller Warren Jacksonsaid.
For long time Top Enders who think they've seen it all but Jackson said now was no time for complacency.
"One of our worst fears is that people get complacent, especially those people who've been in Darwin and the region for a long period of time," he said.
"We can't be sure of what will actually happen, that's the end result so we need to be prepared for anything."
- AAP
