One organization that made the list is called Church Initiative located in Wake Forest. It refers to itself as a non-profit business that produces videos and sells published material.
Their website states it offers strategic ministry for people experiencing a life crisis, like divorce and loss of a loved one.
"Noble cause, but I don't think it's a religious purpose," Wake County Revenue Director Marcus Kinrade said. "So we actually removed their exemption."
Church Initiative says it had been exempt from property taxes for the last decade, but Wake County now says the group owes more than $10,000 for 2009 on their $1 million piece of real estate.
"Just because they are churches does not mean they are exempt," Kinrade said. "The property or land has to be used for a religious purpose."
Meanwhile in Cary, Sha'Arei Shalom Messianic Jewish Congregation thought they were tax-exempt, too.
However, Wake County says they are also late on $10,000 in 2009 property taxes.
More than 50 families have been worshipping at the temple for the last year. It was a Christian church before that.
Apparently, a mix-up in a mailing address is the reason they are being charged property taxes now.
Wake County says there's no local exemption for churches or synagogues missing a filing deadline for tax-exempt status.
"Once we get outside the calendar year, they can't apply for exemption anymore for that year, and the bill has to be paid," Kinrade said.
Both the Church Initiative and the Cary synagogue are filing appeals with the state, but that process could take another year.