The announcement from the kingdom's Communications and Information Technology Commission (CITC) follows local newspaper reports last week that claimed the government had asked telecom companies to look at ways to monitor or block these services.
"It has become evident that some communication applications through (the) Internet don't meet regulatory requirements," CITC said in a statement on its website. "The authority has informed licensed (telecom) providers of the need to work with the developers of these applications to quickly meet these requirements."
The statement listed Voice over IP (VoIP) providers Skype and Viber as well as Internet-based instant messaging service Whatsapp.
But it did not state what laws these applications had flouted, how long they would be given to comply with the regulations or what action would be taken if they failed to heed the instruction.
The CITC said it was acting to "protect society from any negative aspects that could harm the public interest".
Saudi's three mobile operators - Saudi Telecom Co, Etihad Etisalat (Mobily) and Zain Saudi - were not immediately available for comment.