The Pentagon on Wednesday ordered a 21-day quarantine for all troops returning from West Africa as controversy raged over the US government's attempts to prevent the spread of Ebola.

The move exposed a split between the Ebola response from the US military and from other government agencies, with civilian health workers subjected to less strict measures than American soldiers.

Defense Secretary Chuck Hagel's decision came amid a growing debate about the government's handling of the crisis, with some medical experts accusing some US states of taking draconian measures with no basis in science.

The case of American nurse Kaci Hickox, who recently returned from Sierra Leone and was quarantined for several days in an outdoor isolation tent at a New Jersey hospital, remained at the center of the furor.

Hickox is now in her home state of Maine, where officials intend to ask her to respect a home quarantine. But the nurse has said she will take action unless the restrictions are lifted by Thursday.

"I will go to court to attain my freedom," Hickox, who worked for Doctors Without Borders in Sierra Leone, told ABC via Skype from her home in Fort Kent, Maine.

"I have been completely asymptomatic since I've been here. I feel absolutely great."

Hickox, 29, was quarantined after arriving at Newark international airport despite showing no Ebola symptoms. Hickox said she believes the temperature that officials cited for her quarantine was incorrect.

President Barack Obama has been criticized for moving too slowly to counter the outbreak but he has appealed for calm, making a point of thanking American health workers who have traveled to West Africa to treat Ebola patients.

He said his administration's approach was based on "science, not fear" and argued the best way to protect Americans was to stop the virus "at the source" in the hard-hit countries of Guinea, Liberia and Sierra Leone.

- Arguing over quarantines -

Obama's deputies clashed with the governors of New York and New Jersey in recent days after the states announced strict 21-day quarantines for travelers who had direct contact with Ebola patients.

But the governors appeared to ease off the measures this week, though there was confusion over exactly how the rules would be carried out.

New York Governor Andrew Cuomo denied his actions could discourage badly needed doctors and nurses from heading to West Africa.

"I'm looking to encourage doctors to go. At the same time, I want to protect the public health here in New York," Cuomo told the Fox Business Network.

He and New Jersey Governor Chris Christie had jointly ordered the quarantine measures because "we want to err on the side of caution," Cuomo said.

The Pentagon also cited "an abundance of caution" for its decision to impose a three-week quarantine on soldiers returning from Liberia and Senegal.

But the move contradicted the policy outlined by the Obama administration's top health officials. And the State Department said it had no similar plan for a quarantine on diplomats returning from West Africa.

In what Defense Secretary Chuck Hagel called a "prudent" measure, the order directed all branches of the military to place troops arriving back from West Africa in isolation for three weeks.

- Families back strict measures -

The quarantine was introduced even though officials say the soldiers will be focused on building medical clinics or training and will have no contact with those infected with the virus.

But Hagel said the decision was taken partly because military families urged the quarantine.

The US Army had already ordered a quarantine for its troops coming back from Liberia. Hagel's order extended the measure across the military. There are now about 1,100 US troops in Liberia and Senegal, with plans to boost the force to as many as 4,000 soldiers.

Only two people have been infected with the virus on US soil, and both have been declared cured.

The one patient who has died of Ebola in a US hospital was a Liberian, Thomas Eric Duncan.

Another patient, American doctor Craig Spencer, is still being treated for the virus at Bellevue Hospital in New York. Spencer had treated Ebola patients in Guinea.