Olivier David Och, 31, and Daniela Widmer, 28, were abducted on Friday while driving through impoverished and sparsely populated Baluchistan province, which borders both Iran and Afghanistan, in southwest Pakistan.
"We have information the Swiss couple have been shifted to the tribal areas," provincial home secretary Zafarullah Baloch told AFP.
The semi-autonomous region has been dubbed by Washington as the most dangerous place on Earth and a global headquarters of Al-Qaeda.
Parts of the mountainous badlands are subject to American drone strikes against Taliban and Al-Qaeda commanders, and on the ground the region is considered an intelligence "black hole".
Baloch said the couple were probably transferred to the southwestern town of Zhob, but did not specify where precisely they were likely to be now.
He said searches would continue in Baluchistan and that it was still unclear whether they were kidnapped by criminals or militants.
The couple's blue Volkswagen van was found abandoned in Killi Nigah after they were snatched in Loralai district, around 170 kilometres east of the provincial capital Quetta.
According to visas stamped in their passports, they entered Pakistan from India on June 28th.
Officials say that so far, the kidnappers have conveyed no demands.
The pair entered Baluchistan from Punjab province and might have been heading for Quetta, perhaps en route to Iran, officials said.
The Swiss embassy confirmed that the couple had been abducted but that it was "very hopeful that they will be released soon, and safe and sound".
It was the first known kidnapping of Swiss citizens in Pakistan.
Since 2008, Switzerland has advised against non-essential travel to Pakistan, citing risks including the threat of kidnapping.
A French tourist was held hostage for three months in Baluchistan from May to August 2009 while travelling with two other French men, a woman and two children in a camper-van with French number plates from Quetta to Iran.
Baluchistan has seen an upswing in violence recently, suffering from a separatist insurgency, sectarian violence and Taliban militants.
Hundreds of people have died since rebels rose up in 2004 demanding political autonomy and a greater share of profits from the region's natural oil, gas and mineral resources.