(RNS) Members of one of the largest congregations in the Presbyterian Church (USA) have voted to leave the denomination, despite facing an $8.89 million cost for leaving.

Menlo Park Presbyterian is based in the San Francisco Bay area and led by well-known author and pastor John Ortberg. It is the ninth-largest PCUSA church, with about 4,000 members, including former Secretary of State Condoleezza Rice.

The motion to leave the PCUSA was approved by 93 percent of the church’s members who voted, with 2,024 ballots in favor of the motion and 158 ballots opposed, according to a letter posted by Ortberg. Menlo Park determined that to keep its property and leave the denomination would cost $8.89 million, based on a summary for dismissal agreement.

"This is a major milestone, and not an ending but a beginning. There's a lot yet to come of what Dallas Willard called the unique life of spiritual adventure in living with God daily -- entering fully into the good news that Jesus has brought, for ourselves, and for us as a church," Ortberg wrote.

A Menlo Park spokeswoman did not return calls for comment.

The church voted to join a newer denomination called ECO, A Covenant Order of Evangelical Presbyterians, which has attracted 115 other Presbyterian churches since it started in 2012. In its rationale for leaving, Menlo Park cited differences in identity, mission, governance and owning its property.

“Surprisingly, there are many PC(USA)-ordained pastors who do not believe, for example, in the deity of Christ or in salvation through faith in Christ,” the rationale states, citing a 2011 PCUSA survey that suggested 41 percent agreed with the statement, “Only followers of Jesus Christ can be saved.”

The church also cited difference in mission. For example, the local Presbytery of San Francisco adopted resolutions calling for pulling investments in area employers such as Hewlett Packard and Motorola because of their business with the government of Israel. Menlo Park considered the resolutions a distraction from its core mission.

The move comes shortly after a prominent Texas congregation narrowly voted to remain with the denomination. A majority of members at First Presbyterian Church of Houston voted to join the ECO, but the vote fell short of a required two-thirds majority by 36 votes. The church is the seventh largest in the denomination, with more than 4,000 members.

Last year, Highland Park Presbyterian Church, another Texas megachurch of about 4,000 members, voted to leave the PCUSA for ECO, and it remains in a property dispute with the PCUSA.

While not cited in Menlo Park's key reasons for leaving the denomination, differences over sexuality have been a key issue for many departing congregations. The PCUSA’s General Assembly in 2012 upheld the definition of marriage as between a man and a woman, a decision that is expected come up again during this summer’s assembly. In 2010, the denomination moved to drop its ban on noncelibate gay and lesbian ministers.

The PCUSA has 1.8 million members, losing an average of 60,000 per year, according to the denomination. A spokeswoman at PCUSA headquarters in Louisville, Ky., said she would be unavailable to comment before RNS deadline.

KRE/MG END BAILEY