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 an academic 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.
Cambridge University psychologist Aleksandr Kogan, who developed the app used to gather data, insisted he believed what he was doing was "perfectly legal and within the terms of service" of the social network but admitted he regretted not asking more questions about the work.
He claimed CA approached him to do the work, which resulted in the details of around 30 million Americans being collected, but he did not know how that information was used by the data firm.
Dr Kogan developed a personality survey called This Is Your Digital Life.
Crucially, as well as harvesting details of the people who completed the survey it could also access their friends' information, depending on privacy settings on Facebook.
Dr Kogan told the BBC that around 200,000 people were recruited to do the survey and around 30 million users' details were collected.
A whistleblower has previously claimed details of more than 50 million people were harvested.
CA has denied using the Facebook data in its work on Donald Trump's US presidential campaign.
Facebook banned CA from using its platform on Friday and has also blocked Dr Kogan.
But the academic told the BBC's Today programme: "My view is that I'm being basically used as a scapegoat by both Facebook and Cambridge Analytica.
"Honestly we thought we were acting perfectly appropriately, we thought we were doing something that was really normal."
"What happened was, they approached me," he said.
"In terms of the usage of Facebook data they wrote the terms of service for the app, they provided the legal advice that this was all appropriate."
But he said "one of the great mistakes I did here was I just didn't ask enough questions".
Dr Kogan claimed CA's suspended chief executive Alexander Nix was wrong when he told MPs he had not been supplied data by the academic's firm GSR.
Mr Nix told MPs that GSR "did some research for us back in 2014" that "proved to be fruitless".
Asked if that was wrong, Dr Kogan told Today: "I believe it is. I don't see why that would be accurate."
Dr Kogan said he would be prepared to appear before Parliament or the US Congress to give his version of events.
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.
Damian Collins, chairman of the Digital, Culture, Media and Sport Committee, wrote to Mr Zuckerberg on Tuesday requesting that the firm explains the "catastrophic" failure.
CA suspended Mr Nix on Tuesday, after recordings emerged of him making a series of controversial claims, including boasts that CA had a pivotal role in the election of Mr Trump.
The CA board said that Mr Nix had been suspended "with immediate effect, pending a full, independent investigation".