The former president said he had nothing to do with the firm's operation in Nigeria.
A recent report by The Guardian UK revealed that an unnamed Nigerian billionaire paid £2m to the company to influence the vote for Jonathan.
Cambridge Analytica staff were flown to Nigeria and Israeli hackers were hired to break into then-opponent Muhammadu Buhari's emails to exhume his financial and medical records. Staff were also handed videos put together to scare voters in Buhari's stronghold of the north.
The Cambridge Analytica team was alleged to have swiped the data of more than 87 million Facebook users to sway elections in many countries including Nigeria and Kenya.
With the Federal Government set to inaugurate an in-house committee to investigate the activities of the data mining firm in the country's general elections in 2007 and 2015, Jonathan has reacted to the controversy.
According to a report by AFP, the former president's spokesperson, Ikechukwu Eze, said he had nothing to do with the firm's operation in Nigeria.
While answering questions on Thursday, April 5, 2018, Eze said, "He (Jonathan) wasn't aware of it. The best thing to do is to wait for the conclusion of the investigation."
Despite the firm's operation that included a video that displayed graphic violence and portrayed Buhari as a supporter of sharia law who would brutally suppress the people, Jonathan lost the 2015 election to him and didn't contest the results of the election.
The Cambridge Analytica team were lodged in a hotel in Abuja a few weeks to the presidential election and worked on a communications campaign for Jonathan.
The Israeli intelligence operatives who worked with Cambridge Analytica during this period claimed that France and Israel wanted Jonathan to win the presidential election.
The Guardian, citing former Cambridge Analytica employees, had reported that during the election campaign, the UK firm was offered materials from Israeli hackers.
The ex-employees reportedly described how the hackers passed a thumb drive of hacked material relating to Buhari to them in Cambridge Analytica's offices and they were directed by Alexander Nix, its chief executive, and Brittany Kaiser, a senior director, to search Buhari's personal emails for compromising material that could be used to smear him.
Even though The Guardian UK reported that Jonathan was most likely unaware of the hiring of Cambridge Analytica, his name has been dragged through the scandal.