Kenyatta's win was yesterday declared "invalid, null and void" by four Supreme Court judges, who cited irregularities "in the transmission of results".
A fresh election has been ordered for October. But Kenyatta, after initially calling for calm, has responded by saying "we clearly have a problem" with the judges who made the ruling.
Speaking at a party meeting at his official residence, Nairobi's State House, Kenyatta criticised the judges' decision and said he would return to the issue if re-elected.
He said: "We shall revisit this thing. We clearly have a problem. Who even elected you? Were you? We have a problem and we must fix it.”
Kenyatta argued that the results of members of parliament, senators and governors were transmitted through the same system of the country's Independent Electoral and Boundaries Commission(IEBC) and "no one asked any questions".
He continued: “The Supreme Court sat and decided that they are the ones with a bigger power than the 15 million Kenyans who woke up, queued in lines, and voted for their preferred presidential candidate. As a Supreme Court, they cannot annul the wishes of the people. And we will revisit this thing.”
Analysts saw the president's latest comments on the judiciary as a worrying development.
"It's extremely unfortunate that Kenyatta seems to be issuing veiled threats at the judiciary," said Murithi Mutiga, a Nairobi-based senior Africa analyst at the International Crisis Group.
The election annulment came after the main opposition party, the National Super Alliance (NASA), filed a petition to the country's Supreme Court to overturn the result, and unexpectedly won by four judges to two. Chief Justice David Maraga said the presidential election was unconstitutional.
Opposition leader Raila Odinga hailed the result as a “historic day for the people of Kenya and by extension the people of Africa”.
But he also expressed concern over the integrity of election officials, calling for some to be prosecuted, and said it was "unimaginable" a new poll could be conducted in just two months.
Following the landmark judicial ruling, Kenyatta first struck a conciliatory tone, saying: "Your neighbour will still be your neighbour, regardless of what has happened. My primary message today to every single Kenyan is peace. Let us be people of peace."
The country was ravaged by post election violence in 2007, which left 1,200 people dead and another 600,000 displaced.
But later on Friday, he told a rally of supporters the judges were "crooks" and said Chief Justice Maraga "should know that he is now dealing with the serving president ... We are keeping a close eye on them." Kenyatta's latest comments have added to anxieties over the potential fallout of the annulment.
Ahmed Salim, Vice President of consultancy Teneo Intelligence, said in a note to clients on Friday that the Kenyan court ruling will likely increase tensions between now and the 1 November deadline and the IEBC may even be inclined to hold the elections sooner rather than later.
"The ruling will undoubtedly galvanise the opposition and Odinga supporters, and although the ruling strengthens Kenya’s institutions, public trust towards the electoral commission is completely lost. Any result that does not see Odinga as the victor may result in violence and unrest," he said.
Salim said the court’s decision is embarrassing for Kenyatta because it discredits his campaign and makes it appear desperate considering how highly critical it was towards the courts and the chief justice.
"The real risk between now and the next election will be state-sponsored violence and intimidation, particularly as Kenyatta’s allies realise that they may lose the presidency," he warned.
"More broadly, this also raises the question of whether the electoral commissioner’s ICT manager was killed by the state. The short-term impact on the economy will be negative due to the immense political uncertainty."
Meanwhile, the Kenya Magistrates and Judges Association yesterday condemned Kenyatta’s attacks and threats on Supreme Court judges following the ruling on Odinga’s petition. They have asked the political class to desist from personal profiling of judicial officers who are engaged in their constitutionally ordained duties.
The association further hailed the Supreme Court of Kenya for delivering on its mandate despite the strict timelines, bulky pleadings, evidence and submissions which they had to critically analyse.