The blocking of Al-Saiha comes after it published on Sunday commentary critical of Bashir's national dialogue.
The dialogue, announced in January, is aimed at resolving multiple crises in the impoverished, war-ravaged nation. But the arrest of political figures and continued press censorship has raised questions about the regime's commitment to reform.
"Our newspaper was suspended indefinitely" by state security agents, Al-Saiha publisher Al-Tayeb Mustafa told AFP.
The daily returned to the streets yesterday after a ban lasting weeks.
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A Sunday column by Mustafa criticised the government's handling of the dialogue.
In a separate interview with Al-Saiha yesterday, Ghazi Salahuddin Atabani, head of the Reform Now opposition party, voiced numerous criticisms including of the parliament which recently revoked his membership.
Reform Now had initially agreed to join Bashir's dialogue but then said the process could not continue until Al-Saiha was allowed to resume publishing, and a detained opposition chief was released.
Mustafa launched Al-Saiha after complaining he was forced out of Sudan's largest newspaper, Al-Intibaha, in a dispute with the regime he called "a military dictatorship".
"I think we fulfilled our commitment when we published yesterday, but they decided to suspend us," he told AFP.
On Saturday, security agents seized all the copies of another daily, Al-Tayar, after it reported a cabinet minister's anger at delays in the national dialogue, Al-Tayar's chief editor said.