The money quote from the Al Hayat interview, which neither Reuters nor AFP published, was this:
Moderate Islamists who were harshly suppressed by secular Arab dictators have gained political power or prominence following popular uprisings in Tunisia, Libya and Egypt.
But armed, militant Islamist groups, including the North African wing of al Qaeda, have also benefited from lapses in internal security across the region wrought by the often chaotic transition to more democratic government.
Marzouki told pan-Arab daily al Hayat that some of Tunisia's hardline Salafists had links to al Qaeda and that North African countries would work before the end of the year to form a united front against the threat of rising Islamist militancy.
"The centre of the terrorist movement is moving now from Afghanistan and Pakistan to the Arab Maghreb region ... and the great danger is at our doors," Marzouki said.
He said around 3,000 Salafists in Tunisia were estimated to be potentially dangerous and described them as a "cancer" in the country, the first in the Arab world to bring down dictatorship in a wave of popular uprisings.
Marzouki, a secularist in office under a power-sharing deal with the moderate Islamist Ennahda party after it won a free election a year ago, said talks with such militants were futile and the threat they posed must be addressed with legal measures.
"(Militants) are mainly present in Libya and Algeria, and especially in the south," Marzouki said, referring to the remote and thinly populated desert expanses of the Maghreb where policing is weaker and there has been traditional tribal resistance to central authority.
"There is a security problem now threatening the entire Arab Maghreb region ... All our southern borders are threatened with this problem now. There has to be a unified response from all the countries."
The rise of Islamist parties in the "Arab Spring" countries are a "poisoned gift," he said, pointing out that the Arab peoples had big ambitions beyond the current reality.While the relatively moderate Ennahda party in Tunisia was forced to share power with Marzouk's secularist party, in Egypt the Muslim Brotherhood and the Salafists achieved an overwhelming majority in the parliamentary elections. So the Salafists that he is warning against in the Maghreb as being potential terrorists are the same ones who are now hugely influential in the Arab world's most populous nation, and helping write the constitution there.