Gandhi had made a similar allegation Wednesday when he began his two-day Rajasthan trip, which happened to coincide with the shake-up at the Central Bureau of Investigation.
Finance Minister Arun Jaitley has already dismissed as "rubbish" allegations that CBI director Alok Verma was sent on leave because he wanted to investigate the Rafale deal.
On Thursday, talking to Mahila Congress workers in Kota and at a rally in Sikar, Gandhi brought up Rafale and the CBI again.
He also mocked Modi over an earlier remark that he wanted to be the country's watchman against corruption.
“Two days ago the watchman did something new,” the Congress chief said.
“It was not done in the daytime, but when people of the country were sleeping,” he said, referring to the government decision on the CBI.
“I feel sad that one watchman has defamed all watchmen of the country. These watchmen are not at fault as they are working honestly. We are talking about an individual who had asked to be made a 'chowkidar' rather than the prime minister,” Gandhi said at the 'Maha Sankalp' rally in Sikar district.
“The CBI was going to start an inquiry and therefore the prime minister got scared and removed the CBI chief at 1 am in the night,” he said in Kota.
Gandhi repeated the allegation that the prime minister paved the way for Anil Ambani's Reliance Group to bag a Rafale-related offset deal. Both the government and the Reliance Group have earlier rejected the charges.
Gandhi also mentioned the sacrifices of Army jawans from the state's Shekhawati region, linking them again to the fighter deal with France and the alleged favouritism towards the Reliance Group.
He repeated the Congress allegation that the Rafale jets were being procured at a much higher price than what was being negotiated while the UPA government was in power.
He claimed the Defence Ministry and the Indian Air Force were not consulted.
“The defence ministry and the IAF worked for years on the contract. But the prime minister, without asking the defence minister or the defence ministry or the IAF, changed the contract of Rs 30,000 crore,” he said.
A late-night order on Tuesday from the Appointments Committee of the Cabinet led by the prime minister sent Verma and CBI Special Director Rakesh Asthana, who were at loggerheads, on leave.
Jaitley said on Wednesday that the government's decision to remove the CBI's two top officers was based on the Central Vigilance Commission's (CVC) recommendations.
Gandhi pushed for the participation of more women across various levels in the Congress, saying he would like half of his party's chief ministers to be women in the next five to seven years.
Manvendra Singh, who recently switched from the Bharatiya Janata Party to the Congress, was present on the stage.