A man who burglarized a Huntington Station convent twice last month was arrested Tuesday and charged with two counts of second-degree burglary as a hate crime, police said.

Suffolk County police said Roberto Pantoja, 31, of East Fourth Street, Huntington Station, was arrested after an investigation by Hate Crimes Unit detectives.

Pantoja’s bail was set at $40,000 cash or $80,000 bond after his arraignment Wednesday in First District Court in Central Islip. Additional arraignment information, including the name of Pantoja’s attorney, was not immediately known.

On March 7 and again on March 26, police said, Pantoja entered the St. Hugh of Lincoln Convent on East Ninth Street and stole property and cash belonging to nuns who live there.

Police declined to detail what type of items were stolen — or their value — and said only that Pantoja was charged with a hate crime because he targeted the convent “because of the religious practice of the people who live inside.”

Suffolk Det. Sgt. James Brierton of the Hate Crimes Unit said police interviewed Pantoja and “he gave us enough of a probable cause to add the hate crime element to the charge of burglary.”

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Brierton declined to reveal what Pantoja told authorities.

The convent is associated with the Roman Catholic Church. St. Hugh of Lincoln lived in the 12th century and was the patron saint of sick children, sick people, shoemakers and swans.

Brierton said physical evidence recovered from the scene helped police identify Pantoja as a possible suspect.

The investigation is continuing, police said, and detectives said anyone with information about the case should contact the Hate Crimes Unit at 631-852-6323.

With Darran Simon