Hughes was appointed the second Bishop of Metuchen in New Jersey on December 11, 1986, and was installed on February 5, 1987. He reached the retirement age of 75 on November 13, 1995. When his resignation was accepted by the Holy See on July 7, 1997, he became bishop emeritus. He was outspoken in his beliefs against racism and abortion.[3] Hughes continued to perform confirmations and celebrate Masses throughout the Diocese of Metuchen for many years after his retirement. He died on December 25, 2012, at the age of 92.[4]
In November 2020, a Vatican investigation into the case of defrocked former cardinal Theodore McCarrick identified Hughes as one of three bishops who "provided inaccurate and incomplete information to the Holy See regarding McCarrick’s sexual conduct with young adults" when McCarrick was a candidate for the post of Archbishop of Washington in 2000,[5][6] though Hughes' conclusion was that it would be "unwise to consider the Archbishop for any promotion or additional honor".[7]