Mora alleged that Ramirez met his Pacific cartel contact in Mexico City twice and that, at the second meeting, Ramirez was reportedly accompanied by two other directors of his agency's organised crime division.
The two others, Miguel Angel Colorado and Fernando Rivera, were also arrested, AP reported.
Ramirez was named assistant attorney general for organised crime in 2006 after Felipe Calderon, the president of Mexico, took office, and resigned in July at Mora's request.
Calderon has pledged to crack down on Mexico's drug cartels and corruption within the security force and political establishment, but violence has increased dramatically.
In the past two years, under Mexico's "Operation Clean House", Calderon's bid to wrest territory from the grip of drug cartels, more than 25,000 army troops and federal police have been deployed across the country.
With Ramirez's arrest, five top officials and two federal agents have been detained this year as part of the operation.
Mora said the Mexican government remained determined "to purge federal security and judicial institutions, identifying people who ... are involved in criminal
activities and have abandoned the principles and values of public service".
"We will not betray the trust the President Felipe Calderon has given us," he said.
Authorities also arrested 35 employees of the organised crime unit last month on charges of passing information to the Sinaloa drug cartel.
Around 4,000 people have been killed in Mexico in drug-related attacks so far this year. Many of them had been severely tortured or decapitated.