Speaking to Al Jazeera Reverend Lawrence Andrew, editor of The Herald, said he was happy the government had renewed the weekly's 2008 permit without any conditions.
"The renewal process usually takes two to three months but I don’t know what caused the delay this time," he said.
"The government did not give any explanation in its letter."
Print publications in Malaysia require a government permit which is renewed every year.
The government has previously warned The Herald, which has a circulation of 12,000 among Catholics, that its permit could be revoked if it continued to use the word "Allah" for God in its Malay-language section.
"Allah" is Arabic for God and means the same in Malay, Malaysia's national language.
Christians in Malaysia have argued that the word "Allah" was used by Christians before Islam.
Andrew said he did not know the reason for the initial ban, which the Herald had appealed.
"It could have been due to any of the articles we have published, and not necessarily the use of the word Allah," he added.
Andrew said people cannot be denied the use of their language, adding that the community is grateful the ban was not imposed.
"It was certainly a good thing for the country as a whole that we can accept one another. We need to be moderate and have tolerance," he added.
Early this month The Herald filed a suit seeking a declaration on the use of the word "Allah" as a constitutional right.
Meanwhile, in a separate development it has emerged that a church in the eastern state of Sabah is also suing Malaysian authorities for barring the import of Christian literature from Indonesia containing the word "Allah".
Sabah Sidang Injil Borneo Church filed the case in Kuala Lumpur earlier this month after six titles for their Sunday school education for children were banned.
Letters from the internal security ministry said the books contained various words that were exclusive to Islam, including "Allah" (God), "Baitullah" (House of God), "Solat" (prayer) and "Kaabah" (The Sacred House).
In multi-racial Malaysia, the government considers religion a sensitive matter and often classify related matters as a security issue.