Meteorologists have warned that Monica may intensify again before menacing Western Australia.
The storm was packing winds of up to 350kph near its core when it touched down on Monday night at Maningrida, but weakened significantly and is now classified as a tropical low.
The storm travelled further south and further inland than predicted, sparing Darwin what had been feared would an even more destructive storm than Cyclone Tracy that devastated the city in December 1974, however the city received rain and winds of up to 60kph.
Many Anzac Day events were cancelled, including the march, dawn service and mass at St Mary's Cathedral, the popular horserace meeting at Fannie Bay and the traditional cricket matches at World War II Strauss airstrip, but there was a small group at the Darwin Cenotaph at dawn.
"There's no damage that I'm aware of in Darwin ... for Darwin you could say that (it was a non-event)," said duty forecaster Jenny Farlow.
But smaller communities in the territory were not so lucky.
At Maningrida, on the coast of Arnhem Land, the school, which was being used as a cyclone shelter, sustained damage to some parts of its roof but the people using the shelter had moved to other
parts of the building.
Most buildings in the community suffered some level of leakage and one clad home collapsed off its stilts. It was unoccupied at the time.
"Maningrida probably suffered the worst and the brunt of severe tropical Cyclone Monica," NT Police Commander Bert Hofer told the Seven Network.
"There was substantial infrastructural damage."
Goulburn Island was evacuated, with 348 people transferred by air to Jabiru and then by bus to Pine Creek.
The town of Jabiru was lashed by rain and wind in the early hours, with 12 houses unroofed and damage caused to others by fallen trees.
Many trees are down throughout Kakadu National Park, blocking roads.
Heavy rain was also expected to cause flooding of low-lying areas across the Top End and extend to the northern Kimberley in WA on Wednesday or Thursday.
Cyclone Monica was expected to redevelop over the next 12-18 hours as it moved towards the Kimberley coast, forecasters warned.
"Once they go over the warmer waters this fuels them - they reintensify," Ms Farlow said.
"The steering is in that south-west direction to Western Australia - that top bit there will be affected."
She said Monica has the potential to intensify beyond a category two cyclone before potentially striking the WA coast.
"A cyclone watch is current between the Daly Mouth River right through to the Kimberley," Ms Farlow said.
Destructive winds with gusts of up to 150kph could develop between Kalumburu and the NT/WA border early on Thursday, the bureau warned.