The spike has pushed Malaysia's death toll to among the highest per capita in Asia, even as new infections have slowed in recent weeks amid a ramped-up vaccination programme.
September's figure accounted for more than a third of the 26,335 total Covid-19 deaths reported in Malaysia, which has recorded over 2.2 million infections, the third-highest number in Southeast Asia.
Health ministry officials, however, say the reporting of many deaths have been delayed - some up to several months - as rising cases overwhelmed hospitals and testing labs.
The ministry in September began releasing daily data according to the time of deaths, as well as their reporting date, in a bid to improve transparency and clear the backlog.
Although Malaysia reported a daily average of 322 Covid-19 fatalities in September, actual daily deaths fell to 89 as of Thursday based on a seven-day rolling average, the data showed.
Authorities have pledged to reduce the lags by imposing time limits on hospitals to confirm cause of death.
The previously unreported fatalities exposed systemic gaps, despite Malaysia having one of the fastest vaccine rollouts in Southeast Asia, University of Malaya infectious diseases expert Adeeba Kamarulzaman told Reuters.
These include uneven vaccination rates in different states, inadequate monitoring of Covid-19 patients in home quarantine, as well as limited access to healthcare among undocumented migrants, she said.
"Many in the migrant population either lack information about the disease or fear coming forward for care, in case they are arrested," Adeeba said.
Malaysia also has high rates of obesity, diabetes and hypertension, particularly among younger adults who were vaccinated later, which increased their risk of contracting severe Covid-19 infections, she added.
About 62 per cent of Malaysia's 32 million population are now fully vaccinated, including 86 per cent of adults. The country began inoculating teenagers between the ages of 12-17 last month.