"We do not yet know whether the clinic will obtain admitting and staff privileges," he wrote, adding: "As both parties stated during the hearing, the resolution of that issue will impact the ultimate issues in this case."
Both sides claimed a partial victory in the ruling.
Nancy Northup, president of the New York-based Center for Reproductive Rights, which had petitioned the court for an injunction to the law, said: "The federal judge has provided crucial temporary protection for the clinic and its physicians.
"We will remain vigilant in our fight to ensure the clinic isn't subject to penalties that would force its doors to close and deprive Mississippi women of their constitutionally protected rights."
Meanwhile, Mississippi governor Phil Bryant said Friday he was "gratified" that the judge will allow the law to start taking effect.
"Mississippi will continue to defend this important measure as the legal process moves forward," the Republican governor said in a news release.
The new law was due to take effect on July 1. The clinic won an eleventh-hour reprieve from having to comply with conditions that supporters of the center say were designed solely to force its closure.
Pro-choice campaigners have described the new rules as "medically unjustified".
Doctors at the center note that the number of women who experience a complication during an abortion that requires treatment at a hospital is extremely low – less than 0.3% according to the sexual health thinktank the Guttmacher Institute.
In any case, the clinic has an agreement with a local physician, who will admit the centre's clients should the need arise.
Diane Derzis, owner of the Jackson clinic, has accused social conservatives in the state legislature of putting ideology ahead of women's health.
"There has been no subtlety here – they are proud of the fact that the law would make Mississippi abortion-free," she said in an earlier interview with the Guardian newspaper.
Certainly, top officials in the state have made no secret about wanting to shut the center . Phil Bryant has said on a number of occasions that he doesn't want abortions carried out in Mississippi.
"If it closes that clinic, then so be it," Bryant said in April as he signed the new requirements into law.
If the Jackson clinic were to close, it would force women seeking terminations to travel hundreds of miles and cross state lines to have the procedure performed legally.
The nearest clinics to Jackson are approximately three hours' drive away, with most neighboring states requiring a mandatory waiting period and some, such as Louisiana, requiring two trips.
Derzis has said that if her clinic was to close, it would lead to a rise in vulnerable women going to non-registered abortionists.
At present, the clinic performs almost all of the roughly 2,000 abortions that are performed in Mississippi each year.
Judge Jordan noted in his ruling that the facility is seeking the hospital admitting privileges it needs to survive under the new strict rules.
He wrote that he was blocking the state from imposing penalties arising from non-compliance during the application process as the clinic would face "irreparable injury" if criminal or civil proceedings were allowed to take place.
"Given the highly charged political context of this case and the ambiguity still present, the court finds that there would be a chilling effect on the plaintiffs' willingness to continue operating the clinic until they obtained necessary privileges," he wrote.
Intellpuke: You can read this article by Guardian Correspondent Matt Williams, reporting from New York City, N.Y., in context here: www.guardian.co.uk/world/2012/jul/14/mississippi-abortion-clinic-stay-open