The checks were ordered by the government's top representative in nearby Naples, Francesco Musolino, to inspect progress on restoration of the House of the Guilt Cupids, the House of the Great Fountain and the Fullonica of Stephanus laundry.
Italian authorities fear that the EU's pricey 'Grand Plan for Pompeii' initiative to prevent the Unesco World Heritage site from crumbling could be infilitrated by organised crime groups and subject to fraud.
Among the inspections due to be carried out on Tuesday were checks of all the workers involved in the digs and the equipment being used, as well as video-surveillance systems.
Last August, the Italian government vowed that "not one euro" of the EU restorations funds would end up the hands of the Naples mafia or Camorra.
The 66 hectre ancient Roman site was preserved by volcanic ash when Mt. Vesuvius erupted around 2,000 years ago.
Since 2010, Pompeii has been the object of international outcry following a series of highly-publicised collapses at the site. The crumbling of a portion of the House of the Gladiators in November 2010 led to then-culture minister Sandro Bondi's resignation.
Former prime minister Silvio Berlusconi's government was accused by critics of starving culture of needed funds as the country implemented austerity measures to save tens-of-billions of euros to put its financial house in order.
Scandals involving the mafia siphoning off Pompeii funds or placing its own employees to work at the site spring up periodically.
Italy has pledged to be more vigilant this time, perhaps because a large chunk of the funds come from the EU.
Italy is spending 63.2 million euros to for the Pompeii work, while 41.8 million euros will come from the EU.