Typhoon Soudelor caused flash floods when it hit China's Zhejiang province in the east of the country. The region is known for having a large number of Christians.
Huang Yusong, 77, and Zhou Yanxiang, 81, reportedly died earlier in the week when Yangmei Protestant Church in Wenzhou was covered by water.
It is thought the women had been sleeping on the ground floor of the church.
A local source told ucanews.com: "Their bodies were found a few hundred meters from the church the next morning.
"Four faithful had been staying at the church to defend their cross from removal. The two elderly women slept on the ground floor due to leg and arm pains while the other two slept on the upper floor," said the local who did not want to be named.
It is thought the heavy flooding and rain from the typhoon has taken around 40 lives so far.
Following the deaths, Christians took to Chinese social media to appeal for prayer for the two women, many calling them martyrs.
Over the past few months authorities from the ruling Communist Party have conducted a campaign to remove crosses from churches and religious buildings due to what they are saying is health and safety reasons.
The government has removed more than 1200 crosses across China in the last two years, and has completely demolished several other churches.
