The appeal to lift it was rejected after it came to light that the country's security services imposed the ban.
Revd Yat Michael and Revd Peter Reith were released from prison in Sudan last week but were unable to leave the country, they were first arrested in December 2014 and January 2015 respectively.
Both men, from the Presbyterian Evangelical Church, had been accused of undermining the constitutional system of the Sudanese Penal Code; waging war against the state; disclosure and receipt of official information or documents; arousing feelings of discontent among regular forces; breach of public peace; and offences relating to insulting religious beliefs.
A travel ban had originally been imposed in March this year, and the clergymen appealed for it to be lifted - but were informed that the court had no authority to rule on the issue.
The pastor's lawyers are meeting Sudan's National Intelligence and Security Service (NISS) on Monday in an effort to secure a lifting of the ban.
It has been reported that the NISS were unhappy with the judge's decision to release the men.
Christian charity, Christian Solidarity Worldwide (CSW), is concerned about the extensive powers awarded to the NISS; the ability to hold suspects for four and a half months for investigations were recently expanded even further granting them equal status and power with the Sudanese Armed Forces.
The NISS has also been accused of harassing and repressing human rights defenders, religious minorities, opposition activists and journalists.
Mervyn Thomas, CSW Chief Executive, said, "It is deeply concerning that the travel ban was imposed by a paramilitary body with unfettered powers of arrest and detention.
"Particularly worrying is the fact that the NISS' functions and processes are not subject to judicial review.
"This development may herald a new phase in the mistreatment of Reverends Michael and Reith, who instead of being held in prison are now being detained in Sudan against their will.
"As local efforts to assist the clergymen continue, CSW calls once again for urgent interventions with the Sudanese presidency from members of the international community who observed this case to ensure the travel ban is lifted and the pastors and their families can leave the country and resume their lives."
