Theresa May told Facebook and Cambridge Analytica to fully comply with investigations into "very concerning" claims about the harvesting of personal data.
Mrs May supported Information Commissioner Elizabeth Denham's probe, saying "people need to have confidence in how their personal data is being used".
The Prime Minister's comments came after Cambridge University psychologist Aleksandr Kogan, who developed the app to collect data on millions of Facebook users for CA, claimed he has been made a "scapegoat" in the row.
Mrs May was challenged in the Commons over the Tory party's links to CA's parent company SCL Group.
The SNP's Westminster leader Ian Blackford said the firm "has been run by a chairman of Oxford Conservative Association, its founding chairman was a former Conservative MP, a director appears to have donated over £700,000 to the Tory Party, a former Conservative Party treasurer is a shareholder".
The Prime Minister said that "as far as I am aware" there were no current Government contracts with CA or SCL.
She said the CA allegations are "clearly very concerning", adding: "I would expect Facebook, Cambridge Analytica and all organisations involved to comply fully with the investigation that is taking place."
The backlash against Facebook over its handling of personal data has seen calls for users to delete their profiles and wiped billions of dollars off the social media giant's market value.
In an indication of the backlash against Facebook, WhatsApp co-founder Brian Acton appeared to add his voice to critics of Facebook following the row, tweeting "It is time" with the #deletefacebook hashtag.
Along with WhatsApp co-founder Jan Koum, Mr Acton sold the app to Facebook for 19 billion dollars (£11.4 billion) in 2014.
Facebook founder Mark Zuckerberg was called on to explain the company's data protection procedures to MPs in person.