The governor continued, "In no way am I affixing blame for the bomb scare on tens of thousands of United Methodists of steadfast faith and good will throughout West Virginia.
"Instead, my frustration arises from the activists in the church hierarchy who pushed for official approval of a resolution that was oversimplified, unnecessary and divisive," he said.
Underwood also encouraged church involvement in some social issues, but only in limited ways.
"With thousands of West Virginians struggling in poverty because of traps of illiteracy and poor health habits, I believe churches should become increasingly active in addressing the needs of our citizens," the governor said.
Underwood encouraged churches to get involved in the Mission West Virginia program, which adopts families that are moving off welfare rolls to the job market.
"Such a commitment through Mission West Virginia - a privately supported initiative that I established a year ago - would help our families gain independence and fulfillment."
But also on Friday, Methodist church spokesman Tom Burger pointed out that this year's church conference passed two other resolutions critical of Underwood policies. Both concerned the state's program to move people off welfare.
One resolution urged the state to count education and training as "work-related activities" for the purposes of the West Virginia Works program. This would allow people to continue receiving welfare benefits while they go to school or are otherwise trained to get better jobs.
The second urged the state Department of Health and Human Resources to stop counting Supplemental Security Income benefits as income for purposes of the welfare benefit cutoff threshold. This would mean families with disabled members - including many children - could continue receiving SSI and not be penalized by being cut off welfare benefits at the same time.
That resolution states that "God has called the Church to 'preach good news to the poor ... proclaim release to the captives and recovering of sight to the blind, to set at liberty those who are oppressed, to proclaim the acceptable year of the Lord.'"
Burger noted that neither of those resolutions has received any criticism from the governor.
Ann Garcelon, press spokeswoman for DHHR Secretary Joan Ohl, said the agency had no problem with the Methodist church voicing its opinion on welfare issues.
"Not that I've heard, anyway," Garcelon said. "I haven't heard Joan say that the church or anybody else should stay out of this.
"We take anyone's suggestions or recommendations and review them."