* Toure loyalists held overnight
* Microsoft “Africa Chairman” named caretaker PM
* Junta gives no reason for arrests
* Interim President Traore complains to coup leader (Adds caretaker president’s comment, EU statement)
By David Lewis
BAMAKO, April 17 (Reuters) - Mali named a leading scientist as its caretaker prime minister on Tuesday but its path back to civilian rule after last month’s coup was thrown into doubt as soldiers arrested key allies of the ousted president, Amadou Toumani Toure.
The coup emboldened Tuareg-led rebels to seize control of the northern half of the West African country, a zone larger than France which security experts now fear could become a haven for al Qaeda allies already operating largely unchecked there.
The appointment of former NASA astrophysicist Cheick Modibo Diarra, a political novice whom U.S. technology giant Microsoft Corp named its “ambassador to Africa” in 2006, was announced in a brief statement by state television.
The move was the latest step in restoring constitutional order after leaders of the March 22 coup formally handed power to a caretaker president, former parliament speaker Dioncounda Traore, last week.
But the overnight arrests of leading Toure allies by soldiers underlined that the junta holds sway in the capital Bamako, and suggested that the road back to full civilian rule and new elections could be long and rocky.
Those arrested include former prime minister Modibo Sidibe, ex-defence minister Sadio Gassama, Toure’s former chief of staff, General Amadou Cissoko, and Bani Kante, a businessman who advised Toure on Libyan investments in Mali.
“Modibo was arrested at his home by military police around 11 p.m. on Monday evening, the three others were arrested later,” said an aide to Sidibe. The former prime minister has already been detained and released twice since the coup.
A government source said military officers had also been detained as part of around 10 arrests overall. It was not immediately clear who these were.
A third source said the detainees were being held at the barracks just outside Bamako that the junta has made its headquarters.
Separately, a spokesman for ex-finance minister Soumaila Cisse said he too had been arrested and taken to the barracks later in the day. Cisse had been planning to stand as president in elections that were due to take place later this month.
Interim President Traore said he had contacted coup leader Captain Amadou Sanogo about the arrests. “I immediately got in touch with Captain Sanogo to tell him that in a state where the law prevails this is not how things should be done,” he said.
Traore said the reasons for the arrests should be made known and those detained eventually released.
There was no comment from the junta. Sanogo had issued a statement on state television late on Monday saying that the military was targeting several “cases”, which it would pass on to the judiciary.
Northern Mali remains in a precarious limbo after rebels seized all the main towns, including the ancient trading post of Timbuktu, in the space of 72 hours at the start of the month.
The Tuaregs’ secession bid has been ignored abroad and they are now jostling for control of the zone with Islamists whose goal is to impose sharia, or Islamic law, across Mali.
Mass pillaging of food stocks and other necessities during the rebel advance has exacerbated the plight of northerners already facing a food crisis following a drought in the Sahel zone on the southern rim of the Sahara.
In a statement, EU foreign policy chief Catherine Ashton said the EU had more than doubled its humanitarian aid budget for the Sahel for 2012, and was also committed to preserving the unity and sovereignty of Mali. “A way must therefore be found to restore governance and democracy to the north,” she added.
Civil rights groups have cited widespread anecdotal reports of abuses of the local population, including rapes and killings.
With Mali’s own army in disarray, neighbouring countries in the 15-state ECOWAS grouping have signalled they are ready to send troops, but only with a mandate to prevent further rebel advances rather than help Mali to win back lost territory.
In theory, Interim President Traore has 40 days to organise new elections, but many observers say the lack of security in the north will make a vote impossible by then.
An accord between ECOWAS and Sanogo on the transition to civilian rule gave the coup’s leader a say in key parts of the process - including the naming of the interim prime minister, who Sanogo stipulated must have no links with Toure’s rule.
“You can see there are two presidents in Mali,” said a party ally of Traore who requested anonymity. “We have got a two-headed beast, which is not good at all for the country.”
As prime minister, Diarra will have to deal not only with Sanogo, a hitherto obscure captain who has so far resisted all international efforts to sideline him, but also with a rebellion divided between secular Tuaregs and Islamists.
That will be light years removed from his experience with NASA, where he was “interplanetary navigator” on projects such as an unmanned mission to Venus, and with Microsoft, where his role was to coach top managers on African-related issues. (Reporting by Adama Diarra and David Lewis; Writing by Mark John; Editing by Pascal Fletcher)