Since Bhutto's death on Thursday, 40 people have killed in rioting and violent protests. Shops, lorries, welfare centres, ambulances and buses have all been torched in the chaos.
"The situation in the country over the next hours and days will be very precarious, particularly in the Sindh province," she warned.
"Our partners in Pakistan are concerned that civil war may erupt and that military rule will be re-imposed further - there is a desperate feeling that it will be really difficult to recover from this tragedy."
She urged Christians to pray for the country, saying, "We have been asked to pray with and for the people of Pakistan, for peace and stability, and hope that others will join us in this task."
The Executive Director of the World Evangelical Alliance's Religious Liberty Commission, the Rev Johan Candelin, worked with Bhutto, 54, extensively over the years to further democracy.
He called her murder "one of the most tragic events in the history of Pakistan".
"After working together with Mrs Bhutto for democracy for several years I can say that her importance for democracy and human rights in Pakistan can never be underestimated," he stated.
Having had a Catholic nun as a home teacher in Pakistan, Bhutto had great respect for the Christian faith and a strong desire to protect all religious minorities, according to Rev Candelin.
"She told me several times that she wanted to work for Pakistan where a Jew could go to the synagogue, a Christian to the church and a Muslim to the mosque - all without any fear," he said. "She was fully aware of the risk she took when she went back to Pakistan, but said that democracy is worth risking one's life for."
Benazir Bhutto's father, Zulfikar Ali Bhutto, became the country's first popularly elected prime minister. He was ousted in a military coup in 1977, however, and later hanged.
In 1988, aged just 35, Bhutto became the Muslim world's first democratically elected woman prime minister. Deposed in 1990, she was re-elected in 1993, and ousted again in 1996 amid charges of corruption she said were politically motivated.
She was laid to rest on Friday in the mausoleum she built for her father.
