The decision to extend the ceasefire from July 2 to October 31 comes days before the United States is expected to announce if it will permanently lift a 20-year trade embargo on Khartoum.
Sudan's official news agency SUNA said Bashir signed on Sunday an order to extend the ceasefire until October 31, describing it as "part of the government's initiative to bring peace to Sudan".
In June 2016, Bashir declared a unilateral four-month truce in the three regions, where fighting between government forces and rebels has killed tens of thousands of people.
The administration of US President Donald Trump is due to decide on July 12 whether to permanently lift the sanctions imposed on Khartoum in 1997 for its alleged support for Islamist militant groups.
Former US president Barack Obama eased the sanctions in January, but made their permanent lifting dependent on Khartoum's progress in five areas of concern during a six- month review period that ends next week.
These conditions include improved access for aid groups, halting support for rebels in neighbouring South Sudan, an end to hostilities in Darfur, Blue Nile and South Kordofan, and counterterrorism cooperation with US intelligence agencies.
Similar conflicts also erupted in Blue Nile and South Kordofan states after neighbouring South Sudan broke away in 2011.
At least 300,000 people have been killed and 2.5 million displaced in Darfur since the conflict began, the UN says.
Thousands more have been killed in Blue Nile and South Kordofan.
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