Officials from South Korea's Unification Ministry said the ship docked at the North's port of Sonbong.
The deal requires North Korea to close its nuclear reactor at Yongbyon in exchange for fuel supplies.
A team of 10 UN nuclear inspectors has left Beijing for Pyongyang, to monitor the reactor's shutdown.
"We are en route to Yongbyon facilities," the chief inspector, Adel Tolba, told reporters at Beijing airport before boarding a flight to Pyongyang.
"We have our equipment with us. We will resume our work when we arrive."
The ship - No 9 Han Chang - docked at the North Korean port of Sonbong on Saturday loaded with 6,200 tons of heavy fuel oil.
North Korea agreed in February to end its nuclear programme in return for energy aid and better international relations.
The oil delivery is the first shipment of the one million tons of fuel aid that Pyongyang has been promised in return for disarming.
Officials in South Korea have said they expect Pyongyang to live up to its pledge.
Fuel shipments made under an earlier deal were suspended five years ago.
Talks to resume
North Korea has agreed to give the International Atomic Energy Agency (IAEA) inspectors access to the key sites of the Yongbyon complex, including the five megawatt reactor and the plutonium reprocessing plant.
The head of the IAEA, Mohamed ElBaradei, has said it will take about a month to complete setting up the monitoring equipment, and that the reactor's shutdown could be done in a few days.
Talks involving South and North Korea, Russia, Japan, the United States and China are set to resume in Beijing on Wednesday to map out the next stage of disabling the North's nuclear programme.
North Korea has warned that the disarmament deal could still be undone by US "threats."
North Korea tested an atomic bomb for the first time last year, and has repeatedly said it needs nuclear weapons to fend off a US attack.
Last month an international UN team was given access to the Yongbyon plant for the first time since 2002.
Güncelleme Tarihi: 14 Temmuz 2007, 07:31