The Foreign Ministry expressed worries that the escalating activity could unleash a nuclear arms race in the region.
The statement on Monday comes nearly 10 days after the US announced it was withholding millions of dollars in aid to Egypt over human rights concerns.
Observers, however, have noted that the move is also linked to Egypt's relations with North Korea as the US continues to isolate it economically and politically.
In a phone call in July, President Donald Trump gave a thinly veiled warning to Egypt's President Abdel Fattah al-Sisi to stop its economic cooperation with Pyongyang.
Egypt's condemnation comes as the UN Security Council holds its second emergency meeting in a week on Monday about North Korea after a powerful nuclear test explosion added another layer of urgency for diplomats wrestling with what to do about the North's persistent weapons programmes.
Scheduled after North Korea said it detonated a hydrogen bomb underground on Sunday, the emergency session comes six days after the council strongly condemned Pyongyang's "outrageous" launch of a ballistic missile over Japan.
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Less than a month ago, the council imposed its stiffest sanctions so far on the reclusive nation.
North Korea is "deliberately undermining regional peace and stability," the council said on Tuesday when it rebuked the missile test, reiterating demands for the country to halt its ballistic missile and nuclear weapons programmes.
The North trumpeted "perfect success" Sunday in its sixth nuclear test blast since 2006.
Requested by the United States, Japan, France, Britain and South Korea, the Security Council meeting on Monday could bring additional condemnation and discussion of other potential steps.
British Prime Minister Theresa May called in a statement on Sunday for speeding the implementation of existing sanctions and "looking urgently" at new measures in the council.
The group aimed to take a big bite out of the North Korean economy earlier this month by banning the North from exporting coal, iron, lead and seafood products. Together, those are worth about a third of the country's $3 billion in exports last year.
The council could look to sanction other profitable North Korean exports, such as textiles. Another possibility could be tighter limits on North Korean labourers abroad; the recent sanctions barred giving any new permits for such workers.
The US also suggested some other ideas earlier this summer, including air and maritime restrictions and restricting oil to North Korea's military and weapons programmes.
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