"As with every administration, there will be areas where we agree and work closely together and areas where we will have principled disagreement and strong opposition," he said.
Other bishops offered prayers for Biden while also stating their support for Archbishop Gomez.
Bishop Thomas John Paprocki of the Diocese of Springfield in Illinois said in a statement that while, "It is true that the Catholic Church shares the President's concern for justice in matters of the economy, health care, and immigration," there are several of the president's policy positions "at odds with Catholic teaching about the dignity and integrity of human life."
"In this regard, given the President's public profession of full communion with the Church, I am pleased that Archbishop Gomez has spoken on behalf of all the bishops of the United States," Paprocki said.
"I join Archbishop Gomez and my brother bishops in praying that President Biden will be an effective and virtuous leader of our great nation and that he will truly seek healing and unity, which will necessarily include respect for the God-given freedom of people of faith to practice their religion freely," he said.
Archbishop Nelson Perez of Philadelphia also tweeted that "I share the sentiments of the United States Conference of Catholic Bishops' statement via Archbishop José H. Gomez."
Bishop Michael Burbidge of the Catholic Diocese of Arlington said in a statement, "I ask Catholics and people of goodwill to pray for all elected leaders as they take on the task of carrying out the nation's work."
"We pray also for peace, civility and unity in our nation. The smooth transition of power is a hallmark of our extraordinary American experience and vital to the endurance of our thriving republic," Burbidge said.
Burbidge also offered prayers for Biden's conversion on his public position on the issue of abortion.
"Please pray that our new President will uphold the truths revealed and proclaimed in the Catholic Faith he professes. May the Lord grant him the wisdom and compassion to protect the most vulnerable, especially the unborn; respect the dignity of all people; uphold the traditional family as the foundation of society; defend the principle of religious freedom upon which this nation was founded; and advocate for the rights of the poor," he said.
Bishop Robert Deeley of the Diocese of Portland, Maine, said in a statement, "Every day we should thank God for the blessings of liberty, freedom, and democracy."
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"These are the characteristics of the American experience on full display today in our nation's capital with the inauguration of the 46th President of the United States, Joseph R. Biden, Jr." Deely said. "I join with my brother bishops in congratulating him on his election and inauguration. An inauguration is a beginning. That really means that the work of all of us has just begun as together we build our nation."
Later on Wednesday, Cardinal Cupich released a statement extending prayers and "warmest wishes" to Biden.
"Only two weeks ago, the world watched as our democracy was attacked. Today, we proved its resilience," Cardinal Cupich stated.
"We implore that every life be valued, protected and nurtured as we rebuild a nation once again dedicated to its founding ideals of liberty and justice for all," Cupich stated.
Archbishop Samuel Aquila of Denver also offered prayers for President Biden, support for Archbishop Gomez, and hope that Biden would stand up to his party when it "seeks to advance 'moral evils and threaten human life and dignity, most seriously in the areas of abortion, contraception, marriage, and gender'."
"Advancing the idea that one can have a personal belief that is in direct contradiction with one's public stance, especially on issues that involve the taking of life or the distortion of God's plan for sexuality, is not a mark of integrity and calls for conversion of heart," Aquila said.
