More than 1,800 people have died in eastern Democratic Republic of Congo since Ebola broke out there in August last year.
Mozambique has yet to report an Ebola case, but DRC's regional neighbours have been on high alert while the World Health Organization (WHO) has elevated the crisis to a global health emergency.
Checkpoints began operating in the Milage and Morrumbala districts in the Zambezia province and controls are expected to widen to other provinces of Mozambique that share borders with Malawi, according to a ministry of health official.
"Setting up Ebola checkpoints is a guideline given by decision of the Ministry of Health and World Health Organization to prevent the spread of the disease to other countries" Zambezia province health director, Hidayate Kassim told reporters.
"The checkpoints aim to track all people entering Mozambique having fevers or if they have had contact with anyone who has been in Congo," he said.
"Depending on this control we will determine whether there is a risk or not in our province," Kassim added.
Authorities characterised the screening of people entering Mozambique as a preventive control measure to prepare, prevent, detect and treat any Ebola case that could develop in the country.
The deadliest epidemic of Ebola broke out in West Africa in December 2013 and lasted more than two years, killing more than 11,300 of the 29,000 infected people recorded.
The current one-year old epidemic has left 1,823 dead, according to the DR Congo health ministry, making it second only to the 2013-2016 crisis.
Rwanda on Thursday shuttered its border with DRC after a third case of the deadly virus was detected in the border city of Goma.