Naoto Kan told the Japanese parliament that the combined 9.0 magnitude earthquake, tsunami and nuclear accident were the "biggest crises" in decades.
"From now on, we will continue to handle it in a state of maximum alert," he said.
Mr Kan's comments came after the Tokyo Electric Power Company (Tepco), the operators of the Fukushima plant, confirmed that plutonium had been detected for the first time in two out of five soil samples.
Tepco said the levels of plutonium were not harmful to human health, but experts said the discovery raised concerns that the reactor's containment mechanism had been breached.
"Plutonium is a substance that's emitted when the temperature is high, and it's also heavy and so does not leak out easily," said Hidehiko Nishiyama, deputy director of Japan's Nuclear and Industrial Safety Agency.
"So if plutonium has emerged from the reactor, that tells us something about the damage to the fuel. And if it has breached the original containment system, it underlines the gravity and seriousness of this accident."
It is thought that some of the plutonium may have entered the soil from spent fuel rods at the plant or due to damage to reactor Number 3, the only one using the substance in its fuel mix.
Used in nuclear bombs and a by-product of atomic reactions, plutonium is an extremely dangerous radioactive element.
In spite of the dangers, hundreds of staff and firefighters continued to work in shifts at the plant amid increasingly challenging conditions.
Workers were being given two meals a day – 30 biscuits each and vegetable juice drinks in the morning followed by boil-in-the-bag rice and a can of food in the evening, according to the Mainichi newspaper.
They were sleeping inside blankets in a "key earthquake-proof building", the floors covered with a sheet containing lead to block out the radiation present in the building.
"The working environment is very tough," said Kazuma Yokota, head of the nuclear facility inspection office overseeing the plant.
Japan's government is facing increasing pressure to widen the current evacuation zone, which currently extends to 12 miles from the nuclear plant, even as tens of thousands of residents ordered to leave the area face the prospect that nuclear contamination may prevent them from ever returning home,
"These lands have come from their ancestors and their affection for it is enormous," said Tomo Honda, a member of Fukushima's regional assembly.
"The first step is to actually tell these refugees that they can't go back but people are not facing that reality yet."
An estimated 70,000 people have left the evacuation zone, and a further 130,000 residents living up to 19 miles away have been encouraged to leave or stay indoors.
The government has continued to urge the remaining 40-odd residents who have so far refused to leave their homes within the 12-mile zone to head for safety to avoid damaging their health.
There was also mounting speculation that the government may take steps to nationalise Tepco, which has faced growing criticism for its handling of the situation and was strongly reprimanded by the government for recently miscalculated radiation figures. Koichiro Gemba, the national strategy minister, said the government could consider temporarily nationalising the energy company.
One study claimed that Tepco ignored warnings from scientists and historical researchers in relation to the area's 3,000-year history of strong quakes and tsunamis.
Tepco also reportedly used its own computer programmes to calculate worst case scenario tsunami risks as opposed to an internationally accepted prediction method, according to an investigation by Associated Press.