Sudan, which analysts say is used as an arms-smuggling route to the Hamas-controlled Gaza Strip via neighboring Egypt, said on Wednesday an Israeli air strike had caused a huge explosion and fire at the plant. Israel has declined to comment.
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Black smoke rose from the area of the heavily-guarded Yarmouk factory compound, a Reuters reporter said, but the fire appeared to be small without any explosions in contrast to the large flames and blasts on Tuesday night.
It was impossible to get closer to the gated site.
Firefighters brought the fire under control in a tree-lined grassed area of an industrial zone near the plant, state news agency SUNA said.
"There is no relation to sabotage or an explosion," police spokesman as-Sir Ahmed Omar told SUNA, adding that there were no casualties.
The governor of Khartoum state Abderlrahman al-Khidir said the death toll from Tuesday's strike had risen to four from the previously reported two, state news agency SUNA said. The attack had damaged 35 apartments and other places.
He said President Omar Hassan al-Bashir had ordered him to remove parts of the plant, Sudan's biggest factory for ammunition and small arms, to an area outside the residential area.
Khidir had initially ruled out an "external" reason for the fire on Tuesday night.
In May, Sudan said one person had been killed after a car exploded in the eastern city of Port Sudan. It said the explosion resembled a blast last year that it had blamed on an Israeli missile strike.
Israel declined to comment on the May incident or the 2011 blast, which killed two people and neither admitted nor denied involvement in a similar incident in eastern Sudan in 2009.