BOSTON — A 25-year-old Lowell man, whose drug case was one of 17 drug and firearms cases dropped by prosecutors in the wake of the Lowell police informant probe, filed a federal civil-rights lawsuit Tuesday against the city of Lowell and a veteran Lowell police officer.

Jonathan Santiago, who has no prior drug convictions, alleges that he was arrested on Feb. 21, 2012, by Lowell police Officer Thomas Lafferty after a confidential informant planted cocaine in the gas cap compartment of his car, then alerted police about the drugs, according to the lawsuit.

Santiago alleges that Lafferty, then a detective with the Special Investigation Section, knew the informant planted the drugs but concealed his use of the informant to prevent Santiago and others from learning how the drugs had been placed in the car, the lawsuit states.

Santiago could not be reached for comment, but he told The Boston Globe, “I just couldn’t believe it — that law enforcement would actually do something like this.”

Boston attorney Howard Friedman, who represents Santiago, wrote that Lafferty’s conduct was the result of the city’s “systematic failure to supervise confidential informants within its police department.”

Friedman adds that for more than 20 years, Lowell police ignored its own written policies on the use of informants because the Special Investigation Section believed “the ends justified the means.”

Lafferty could not be reached for comment. City officials were just issued the summons on Tuesday, according to the court docket.

Last month, Lafferty, a 19-year police veteran, and his colleagues in the Special Investigation Section were cleared of any wrongdoing after an independent review showed “no evidence” that two Lowell police informants planted drugs or lied about suspects.

In a joint statement, Middlesex District Attorney Marian Ryan and Essex District Attorney Jonathan Blodgett said the detectives who were assigned to the Special Investigation Section of the Lowell Police Department “did not engage in any criminal wrongdoing or negligence in the performance of their police duties.”

The district attorneys said the detectives did nothing wrong in obtaining intelligence from the informants, and found no evidence that the detectives who were in contact with the informants “knew or should have known of their misconduct.”

The Lowell Police Department currently has in place policies and practices designed to track the accuracy of information provided by confidential informants and to review on an ongoing basis the credibility and performance of its confidential informants, according to the joint statement.

But Santiago’s lawsuit may be the tip of the iceberg, as others whose cases were dismissed or those who had cases involving the two informants, could come forward with lawsuits.

Santiago’s lawsuit alleges “the widespread misuse of confidential informants in the Lowell Police Department.” It also alleges that the city had a “policy or custom of tolerating violations of people’s constitutional rights in order to obtain convictions.”

In his lawsuit, Santiago writes that he was friendly with a man, identified only as “FA,” seeing him occasionally in local bars. FA allegedly was a confidential informant and local drug dealer who had worked with Lafferty and other Lowell detectives for about 10 years, the lawsuit alleges.

On the day of his arrest, Santiago was leaving a friend’s apartment in Lowell when he saw FA, who invited Santiago to join him for a drink at a bar. Santiago suggested they ride together in FA’s car, but FA insisted they each drive their own cars.

Santiago alleges that FA put more than 26 grams of a chunky white powdery substance that included cocaine inside the gas-cap compartment of Santiago’s car. FA either placed the drugs there himself or worked with another confidential informant identified as “FB” to put the substance in a plastic bag inside a sock in the gas compartment, Santiago alleges.

Based on the informant’s tip, Lafferty and other officers were waiting for FA and Santiago to drive by, he alleges. When Santiago was pulled over, Lafferty immediately found the drugs behind the gas cap cover.

Santiago alleges that Lafferty called in a drug-sniffing dog to provide the illusion that the drugs were found without the help of the confidential informant. The police report states that Santiago’s car had “excessive air fresheners” which is a sign of a drug dealer, the lawsuit states.

He maintains there was no mention of a confidential informant being used in this case. Instead, police allege that Santiago was stopped because he was acting suspiciously and that he was driving erratically.

Santiago was charged with trafficking in cocaine over 28 grams, which was later reduced to trafficking in cocaine between 14 and 28 grams after it was tested at the state lab. He was also charged with a school-zone violation because he was near a school when he was pulled over.

The mandatory minimum sentence for trafficking is a three-year state prison sentence with a maximum sentence of up to 15 years.

Santiago was held at the police station for several hours before he was released on bail. In Lowell District Court the next morning, the judge set his bail at $10,000, which was later reduced to $1,000 and he was able to post bail.

The confidential informant probe was triggered when FB approached Massachusetts State Police in hopes of working for that force, too, as informants are often compensated for their information.

The informant told the state police that he was apparently good at “planting stuff.”

State police determined FA and FB were not reliable informants and reported this information to the Middlesex District Attorney’s Office.

On March 6, the DA’s office dropped the charges against Santiago saying it was in the interest of justice. Afterward, Santiago’s criminal defense attorney learned that FB had cited his work planting evidence in Santiago’s car and “bragged about his skill” to the state police, the lawsuit states.

Although the charges against Santiago were dropped as part of the informant probe, Santiago alleges that although he was being framed he “felt fated” to go to prison for a crime he didn’t commit.

After being framed, handcuffed and locked up, Santiago has suffered emotionally, his lawyer wrote.

“For over a year, Mr. Santiago had false felony charges hanging over him… He felt helpless and hopeless, knowing that he had been set up but expecting no one would believe him,” Friedman wrote.

Follow Lisa Redmond on Tout and Twitter@lredmond13_lisa.