South Korea says it has seen no sign that the North is shutting down its main nuclear facility, a key part of a landmark deal reached last month.
Mr ElBaradei is due back in Beijing later on Wednesday
"There is no indication of a change in the operational condition of Yongbyon," said Foreign Minister Song Min-soon.
The deal called on the North to "shut down and seal" its Yongbyon facility within 60 days in return for fuel aid.
Chief UN nuclear negotiator Mohamed ElBaradei is currently in Pyongyang for talks on implementing the deal.
Inspections by the UN watchdog which he heads, the International Atomic Energy Agency (IAEA), are seen as crucial to the success of the agreement, which was reached at six-party talks on 13 February.
Mr ElBaradei has yet to speak publicly about the discussions during his visit to Pyongyang, but he was expected to have pressed the North for a timetable for the resumption of UN inspections.
N KOREA NUCLEAR DEAL
N Korea to 'shut down and seal' Yongbyon reactor, then disable all nuclear facilities
In return, will be given 1m tonnes of heavy fuel oil
N Korea to invite IAEA back to monitor deal
Under earlier 2005 deal, N Korea agreed to end nuclear programme and return to non-proliferation treaty
N Korea's demand for light water reactor to be discussed at "appropriate time"
He will return to Beijing later on Wednesday, where he will brief officials on his trip.
He was reportedly unable to meet with the North's top nuclear negotiator Kim Kye-gwan as planned on Wednesday, because of scheduling problems.
An IAEA spokeswoman said that Mr ElBaradei met instead with another minister, because Mr Kim was busy preparing for forthcoming six-party negotiations.
Six-nation working group discussions resume on Monday in Beijing - involving officials from the US, China, Russia, Japan and the two Koreas.
Under the February deal, North Korea agreed to "shut down and seal" its Yongbyon nuclear reactor within 60 days, in exchange for aid.
The North is to receive 50,000 tonnes of fuel or economic aid of equal value after closing the facility.
A further 950,000 tonnes of fuel oil or an equivalent is to be made available when it permanently disables all its nuclear facilities.
The deal has been welcomed by the international community, especially because of North Korea's nuclear and missile tests last year, which prompted foreign concern and sanctions.
In the past few weeks, delegates from the North have held a series of discussions with other nations involved in the agreement, to move towards implementing the deal.
Mohamed ElBaradei's trip to North Korea is part of that process, and comes more than four years after inspectors with the UN agency were kicked out of the country, when a previous disarmament deal fell apart.