Some of the fiercest battles since February's coup have erupted in Myanmar after Karen ethnic soldiers attacked a Burmese military base.
Heavy gunfire and a spate of airstrikes close to the border also prompted evacuations involving hundreds of Thai residents.
Footage of Tuesday's attack shows the Myanmar military base burning after Karen rebels attacked at dawn.
Stray bullets flew across the river to the Thai side injuring a woman, who needed hospital treatment on her leg.
Forty-year-old Da was sleeping in the village of Mae Sam Laep, Thailand, when the clashes began.
She said they were the worst she has seen in that area for 30 years.
"I heard gunshots and cannon," she said. "Then, the villagers fled, all of us. We couldn't even pack our clothes. Some even forgot their bags and just escaped. Some people forgot to bring their children."
Children, mothers and elderly Thais are among those who authorities have evacuated from their homes.
Some are taking shelter in a local school.
Volunteers told Sky News they have been preparing meals for 450 people but the conflict by the border has left many Thai residents fearing for their safety.
"I'm scared. The villagers are scared too. Just hearing the [fighting] noises makes them frightened," said Supranee Jaikum, 36, a volunteer and employee at the Mae Sam Laep Subdistrict Administrative Administration.
"They imagine many possible accidents, including bomb fragments and bullets."
Myanmar's army has retaliated with airstrikes - bombing rebel-held areas in Karen state (also known as Kayin).
Activists say thousands of Karen locals have hidden in the jungle.
Thai authorities said on Thursday a total of 179 refugees had crossed over since 26 April.
Some 3,000 to 4,000 people fled across the border from Karen in March following airstrikes by Myanmar's army.
The majority have since returned.
The UN estimates more than 40,000 people have been forced from their homes by the escalation in violence in Myanmar, the majority in Karen and Bago states.