A small group of striking teachers attacked the bus as it left Rio de Janeiro for the mountain town of Teresopolis, where the squad will be based during the tournament.
The teachers covered the bus with stickers as Barcelona players Neymar and Dani Alves looked on from inside.
When the bus arrived in Teresopolis, 100kms away, another group of around 30 people chanted anti-World Cup slogans.
"This country's priority shouldn't be the World Cup, it should be improving health, education, housing and public transport," said Rui Costa, a striking teacher who helped organise the protest.
Costa said none of the houses promised to victims of a deadly flood in the area that killed around 1,000 people in 2011 had been delivered.
Protesters allied to a far-left political party held up a banner in English that read, "Billions for the FIFA's World Cup, No housing for the victims of the heavy rains of 2011. Do you think it is fair?"
The demonstrations ended peacefully but they provided another warning of the potential pitfalls that Brazil faces as it struggles to host soccer's biggest extravaganza.
Last year during the Confederations Cup, the dress rehearsal for next month's tournament, hundreds of thousands of people took to streets across the country to protest bus fare hikes.
The grievances soon expanded to cover a lack of social spending and excess investment in football stadiums.
None of the matches were affected but fans fought with riot police outside the arenas and tear gas was used.
"No one here is rooting against Brazil," said Alex Trintino, the coordinator of a local teachers' union.
"This was a symbolic act against a country that doesn't have money for health and education."
The 23 players charged with helping Brazil win a record sixth World Cup title will be based at the refurbished Granja Comary complex on the outskirts of Teresopolis throughout the month-long tournament, the first staged in Brazil since 1950.
Most of the players are scheduled to arrive Monday and undergo a battery of tests before they start physical and ball work on Wednesday.
They face friendlies against Panama on June 3 and Serbia on June 6 and then kick off the World Cup in Sao Paulo against Croatia on June 12.
- Sports & Recreation
- Dani Alves