The unprecedented attacks risk dividing the mainly Muslim nation of 28 million people, which has significant religious minorities, and complicating Prime Minister Najib Razak's plan to win back support from the non-Muslims before the next elections by 2013.
The row, over a court ruling that allowed a Catholic newspaper to use Allah in its Malay-language editions, prompted Muslims to protest at mosques on Friday and sparked arson attacks on three churches that saw one Pentecostalist church gutted.
While Najib visited the badly damaged Pentecostalist church and offered a government grant of half a million ringgit ($148,100) to maintain "a harmonious society," church leaders said they wanted more concrete assurances of safety.
"We ask the government to make a strong statement to these wrongdoers so we can worship in peace on Sunday," Reverend Hermen Shastri, secretary-general to the Council of Churches Malaysia, told Reuters.
Malaysia is mainly Muslim and Malay but there are substantial ethnic Chinese and Indian minorities who mainly practice Christianity, Buddhism and Hinduism.
These minorities handed the government its biggest losses in 2008 state and national elections in part due to feelings of religious marginalization and growing disillusionment with corruption.
In the latest attack on early Saturday, unidentified attackers flung a home-made petrol bomb at the Good Shepherd Lutheran Church in a suburb in Selangor state. The two-storey bungalow sustained minor damage, church officials said.
Police said they have stepped up security at all places of worship but faced a manpower shortage. Inspector General of Police Musa Hasan told churches across the country to hire more security guards.
Christians account for nine percent of the 28 million population, with a sizable number of non-English speaking Christians in Malaysia's Borneo island states of Sabah and Sarawak who have used the word "Allah" for decades.
Najib's handling of the issue will determine whether he can keep the support of the Malays and win back ethnic Chinese and Indian voters to solidify his grip on power after taking control of the government last year.
"Till today we are protecting the interests of other races besides championing those of the Malays," Najib was earlier quoted as saying by state news agency Bernama.
"Don't point fingers and say UMNO is racist...when churches are burned," he said referring to his party, the United Malays National Organization (UMNO) that is the linchpin of the National Front that has ruled the country for 52 years.
But Malay-Muslims, including those in UMNO, fear the word could be used by Christians to proselytize to Muslims, which is already illegal in the Southeast Asian country.
More than 169,000 Malaysians have joined a group page on social networking site Facebook called "Protesting the use of the name Allah by non-Muslims," a fourfold increase from the start of this week that signals growing Islamic anger.