Temer said the authorities were discussing limiting that to between 100 and 200 as the border state struggles to cope with the influx.
"The problem of Venezuela is no longer one of internal politics. It is a threat to the harmony of the whole continent," the President said in a televised address.
More than 50,000 Venezuelans, many of whom are hungry or sick and have little or no money and belongings, have applied for refugee or resident status in Brazil in recent years.
Authorities in Roraima state say that the federal Government needs to do more to help them deal with the growing problems.
Just over a week ago, residents of Pacaraima, a border town in Roraima, hurled rocks at Venezuelans and set fire to their belongings after migrants were blamed for an attack on a local store owner.
Around 1200 were driven back across the border by the violence.
But one Venezuelan who has lived in the area since 2015 and now works with an aid agency said that, despite the difficulties, Brazil was still a better option than Venezuela for many.
"We are coming from a country that's very violent right now," Alba Marina said.
Roraima's state government has tried a few times to shut the border to stem the influx, but the federal Government and courts have so far pushed to keep it open.
Since 2014, an estimated 2.3 million Venezuelans have fled their country's growing humanitarian crisis, including shortages of food and medicine, according to the United Nations.
Some countries, such as Peru and Colombia, see thousands enter each day, and the stream of migrants has strained the resources of countries around the region.
Peru has declared a 60-day health emergency in two provinces on its northern border, citing "imminent danger" to health and sanitation as a result of the migration crisis.
The decree did not give more details on the risks, but the health authorities have previously expressed concerns about the spread of diseases.
Nicolas Maduro, Venezuela's President, has insisted Venezuelans should stop leaving and return to their homeland, which he described as the "country of opportunity".