Alam was called for questioning again earlier in the day, the second time since yesterday, and put under arrest later on, Railway Superintendent of Police P N Mishra told PTI.
Alam, the third term JD(U) MLA from Jokihat in Araria district, was subjected to more grilling after his arrest, the SP said.
His body guard and a personal staff who had accompanied him on Rajdhani Express on January 17 were also arrested along with him.
The Jokihat MLA was released from GRP Patna on five conditions.
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These included depositing his passport so that he can not leave the country during pendency of the probe in the case, the SP said.
Other conditions included he would neither meet the complainant nor apply any pressure on the couple, will cooperate in the ongoing investigation, will acquire a regular bail from a court and deposit two sureties of Rs 20,000 each, he added.
The JD(U) MLA, who is the son of RJD MP from Araria Mohammad Taslimuddin, was allowed to go home last night on medical grounds after four hours of questioning in connection with the case.
The alleged abuse took place on Dibrugarh-New Delhi Rajdhani Express on January 17.
During questioning yesterday, the MLA admitted to travelling in the train on January 17 but claimed he did not abuse the couple.
JD(U) has already suspended Alam in the wake of Rajdhani
The CM while speaking at a function to mark birth anniversary of socialist leader Karpoori Thakur today referred to Alam's incident and reiterated his government and the party will never shield a law breaker.