He expressed "surprise" at the letter as no reference to the supposed court ruling had been made during previous run-ins with the authorities in which the paper had been suspended for long periods.
"We are going to fight back hard and appeal against this decision," he pledged, acknowledging that in the meantime staff had no choice but to comply with the government's order.
The daily angered the authorities only last month with its coverage of a deadly operation by security forces to clear a Khartoum squatter camp housing southerners displaced by the region's long-running civil war.
That edition did not appear on news-stands after the authorities ordered the removal of the report and an accompanying editorial.
Khartoum State Police Commissioner Major General Tareq Osman al-Tahir also ordered "legal measures against the Khartoum Monitor for carrying incorrect news reports" in its edition of May 19.