They entered in three places and descended on the Sunni districts of the coastal city, human rights activists told news agencies.
Communications to the city and surrounding areas appear to have been cut making the reports hard to verify.
Rights activists say more than 580 people have been killed in the uprising since mid-March.
However, Syrian rights group Sawasiah told Reuters news agency on Saturday it has the names of at least 800 civilians who have died.
Syrian officials have given a lower death toll, and say half the fatalities have been soldiers and police, killed by “armed terrorist groups”.
At least 26 people were reportedly killed in Homs, Hama and other cities on Friday, in what protesters had vowed would be a “day of defiance”.
‘Preparing to attack’
Syrian troops and tanks reportedly moved into Baniyas in the early hours of Saturday having circled the city since Wednesday.
Campaigners in touch with residents in Baniyas said the armed units had advanced from three directions on Sunni Muslim areas in the south of the city – steering clear of neighbourhoods of the minority Alawite sect, to which the president and his family belong.
The AFP news agency reported that protesters had formed human chains to try to stop the military operation.
“Residents are reporting the sound of heavy gunfire and seeing Syrian navy boats off the Baniyas coast. Sunni and mixed neighbourhoods are totally besieged now,” one rights campaigner, who did not want to be identified, told Reuters news agency.
Another activist told the Associated Press that tanks were now stationed in at least three Sunni villages just south of Baniyas, and soldiers were carrying house-to-house searches and making arrests.
Hundreds of families were said to be fleeing Baniyas on Friday.
Many feared the city – which has witnessed some of the most persistent demonstrations – would come under siege like Deraa in the south where the uprising erupted seven weeks ago.
The Damascus Center for Human Rights Studies (DCHRS) has accused the government of carrying out “10 days of massacres” as it attempted to take back Deraa.
It says snipers and anti-aircraft machine guns were used to fire on unarmed civilians. Amateur video appears to have shown dozens of unarmed protesters being shot and bleeding to death on the streets.
No reports can be verified independently, as foreign journalists are not allowed into Syria.
The US has called the violence “deplorable” and has pledged a “strong international response” if President Bashar al-Assad does not take steps to end the bloodshed.
The European Union has agreed to impose asset freezes and travel restrictions on up to 14 Syrian officials involved in the brutal crackdown.
The UN says it is to send a team into Syria to investigate the situation, the AP reports.