Tahir took issue with a report that appeared in the paper on Thursday, charging that 17 adults and six children had been killed when police opened fire on civilians in the Soba Aradhi camp, some 10 kilometres (six miles) east of the capital, the previous day.
The police chief said the report was "incorrect and entirely incompatible with the truth".
"For this reason, the state police took the necessary legal action with the prosecution for anti-state crimes," he said.
The outspoken Khartoum Monitor has had repeated brushes with the authorities in which it has been suspended from publication for long periods.
But editor Alfred Taban expressed confidence the paper could mount an effective defence to the latest challenge.
"We have not been notified of this but we can defend ourselves," Taban told AFP. "At least we have the names of the six children and we can easily get the names of the adults."
The paper did not appear on Saturday but Taban said that had not been because of any new suspension.
The authorities "asked us to replace a news report and an editorial, both on the Soba incidents," he said. "We did not have replacements and the newspaper could not appear with blank spaces."