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The Federal Transit Administration (FTA) has fined Metra $90,000 for failing to file federal reports over the past several years. But the federal agency also will lift restrictions on Metra’s access to federal funds for capital projects.

The FTA restricted Metra’s ability to draw federal funds in May 2010 after allegations of misconduct by then-Executive Director Philip Pagano surfaced, prompting the board to put him on leave and launch an investigation.

The FTA followed with an 11-month on-site review of Metra’s practices. As a result, the federal agency fined Metra $90,000 for failing to file reports as required under the Lobbying Disclosure Act. Metra now has filed all past due reports and has rejected its former executive director’s position that no reports were required under the law, Metra officials said in a prepared statement.

Metra’s restricted status was removed after its board took several steps to reform the transit agency’s practices. Those reforms included the hiring of a new executive director and chief executive officer, Alex Clifford; implementing Clifford’s agenda to reform the agency’s practices and procedures; committing to increased transparency; establishing a temporary Office of Inspector General; retaining experts to perform a risk assessment and control analysis; and passing key personnel ordinances to protect whistleblowers and prevent nepotism.

“The agency can now finally turn the page and look forward to a bright future led by our new CEO Alex Clifford, who is bringing updated management practices and customer focus to the culture of Metra, as well as a commitment to transparency and accountability,” said Metra Chairwoman Carole Doris.