Vincent Hoedt, a Dutch aid worker, was arrested a day after his British boss, Paul Foreman, was detained, questioned and charged with offences including spreading false information, before being released on bail.
Speaking in Amsterdam today, an MSF spokeswoman, Susanne Staals, said Mr Hoedt had been arrested in Darfur this morning and authorities were taking him to the Sudanese capital, Khartoum.
Mr Hoedt told Reuters by telephone that he had been arrested but had so far not been charged. Mr Foreman was reported to be meeting the Sudanese authorities today.
MSF said in a statement that the charges facing Mr Foreman were spying, publishing false reports and undermining Sudanese society. The country's attorney-general told Reuters the maximum penalty for the charges was three years in prison and then permanent expulsion from the country.
The Sudanese government was angered by an MSF report, published in March, which said doctors working in Darfur had collected medical evidence of some 500 rapes over a period of just over four months. The report said more than 80% of the victims reported that their attackers were soldiers or members of government-allied militia.
The Sudanese government claimed the report was fabricated after MSF refused its request for medical evidence, citing medical confidentiality.
Jan Egeland, UN under-secretary general for humanitarian affairs, said it was undeniable that rape had been happening in Darfur and said he was "very concerned about the arrests".
Mr Egeland said: "It is an incontestable fact that rape and sexual violence are rampant in the ongoing crisis in Darfur."
MSF described the arrests as "totally unacceptable" and the campaign group Human Rights Watch said today that the Sudanese government should be arresting war criminals in Darfur, not aid workers.
Both Mr Hoedt and Mr Foreman work for the Dutch branch of MSF, which Mr Foreman heads. Mr Hoedt is MSF Holland's Darfur coordinator.
Mohamed Farid, a prosecutor for the Sudanese authorities, said in a statement yesterday that a case had been filed against Mr Foreman and he was asked not to leave the country until interrogations were complete.
Mr Farid said: "Upon interrogation, [Mr Foreman] was not able to substantiate the claims [in the MSF report] nor could he provide any documents to this effect."
The prosecutor complained that the allegations were published on the group's website and quoted by the UN. Mr Farid said if such crimes had really happened the culprits would be punished by prison and fines.
According to Mr Farid, under Sudanese law Mr Foreman should have consulted the country's humanitarian aid commission before publishing the report. It is unclear whether any other relief groups working in Sudan have consulted the aid commission before publishing reports.
Ms Staals said MSF stood behind its report but that the privacy of the sources had to be protected because they had provided information in a doctor-patient relationship.
"We are intrigued by the fact that they are charging us, an agency investing millions in the saving of lives, rather than the people responsible for the rape," said Geoffrey Prescott, another spokesman for the Dutch branch of MSF.
Meanwhile, in Geneva today, UN human rights chief Louise Arbour expressed concern over the Sudanese government's move.
Targeting the humanitarian community for doing its work would "not only do a disservice to the people of Darfur, it will draw attention away from the real criminals, those who continue to rape, kill and pillage with impunity", she said.
The Darfur conflict began when rebels in the region, which is in the west of Sudan, took up arms against what they saw as years of state neglect and discrimination against Sudanese of African origin. The government is accused of responding with a counter-insurgency campaign in which government-backed Arab militiamen known as Janjaweed committed wide-scale abuses - including killings, rape and arson - against the African population.
In more than two years of conflict in Darfur, at least 180,000 people have died, many from starvation.
Read the full MSF report here (pdf).
