The Federal Railroad Administration is cracking down on Metra after three risky situations involving speeding and violating signals -- two during rush hour -- led to three engineers being taken off-duty.
"By acting now, we can help prevent a serious accident where commuters could be hurt," U.S. Transportation Secretary Anthony Foxx said in a statement Friday.
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The routes involved were the Metra Electric and Rock Island lines serving Chicago and the south suburbs.
The government will conduct a 45-day "deep dive safety assessment" of Metra, focusing on how engineers are trained and tested.
Metra "is one of the safest commuter railroads and we want to fulfill those goals (of safety)," Executive Director Don Orseno said. "We will work with the Federal Railroad Administration hand-in-hand.
"This is an anomaly ... it's not something that happens normally."
The safety problems include an engineer passing a stop alert at a signal by about 20 feet at 4:40 p.m. June 3 on the Metra Electric Line.
In addition, there were two cases of speeding, both on the Rock Island Line. The first happened at about 5:15 p.m. May 27 and the second involved an early morning train around 5 a.m. June 2.
Orseno said he could not give details about the speed because of an ongoing Metra investigation and FRA probe.
The probe is similar to "deep dive" assessments of Metro-North Rail, where a fatal crash occurred in the Bronx in 2013. Regulators made 25 recommendations to reduce risks.
FRA investigators intend to interview all affected employees, review event recorder tapes and video recordings and look at Metra locomotive engineer qualifications.
The scrutiny will "provide us an opportunity to assess Metra's testing, training, performance and compliance programs," FRA Administrator Joseph Szabo said.
Orseno said Metra would "turn over every rock, every piece of paper we can find," to explain the safety violations.
The engineers under investigation have lost their certifications while the probe continues. Orseno said about six cases a year of engineers losing their certifications occur on Metra-operated lines. He did not have numbers for Union Pacific and BNSF Line occurrences. In such cases, engineers are taken off-duty until investigations are complete.
As for training, "I can assure you we have one of the finest training programs in the industry," Orseno said.
In a statement this week, Metra spokesman Michael Gillis said "in our preliminary review, we want to assure you that all track, signals and equipment have been tested and are functioning properly.
"As an additional precaution, Metra is issuing a bulletin to all operating personnel to remind them of the importance of safe operating procedures. Agency managers have also been directed to meet with all engineers personally to reinforce the importance of safe operating practices."