The official Middle East News Agency (MENA), quoting an unnamed Egyptian official, on Tuesday repeated the government's position that its nuclear programme was peaceful.
Plutonium can be used in nuclear weapons.
It said Egypt was "completely committed to its agreements" with the UN's International Atomic Energy Agency (IAEA).
It added: "The difference in interpreting some aspects of the safeguards agreement ... led to a failure to inform the IAEA about some experiments and research activities which were undertaken and which are allowed to be undertaken.
"This issue is being dealt with to settle it through complete cooperation and transparency between Egypt and the IAEA, and Egypt is showing good intentions in dealing with the agency in this regard," MENA said.
Western diplomats said on Friday that inspectors from the IAEA were in Egypt to look into a laboratory designed to reprocess plutonium.
They said the IAEA sent the inspectors after learning Egyptian scientists had been conducting undeclared experiments with uranium.
The safeguards agreement between member states and the IAEA, which is headed by Muhammad al-Baradai, an Egyptian, requires disclosure of nuclear materials and periodic inspections to verify compliance.
MENA said most of the experiments and activities concerned were carried out a long time ago.
"We have felt during our discussions with the agency understanding from its side about the limited extent of this issue," it said.
Aly Islam, president of the Egyptian Atomic Energy Authority, on Monday denied inspectors were in Egypt on the date reported by the diplomats.
He said all activities in Egypt conformed with the safeguards agreement.
The diplomats said the undeclared experiments with uranium partly came to light after some of the scientists involved in the project published their research.
They said the laboratory near Cairo may never have been used but added the IAEA was inspecting it to determine whether any work with plutonium had been done there.