The bus company contracted to transport New Haven’s schoolchildren will pay $200,000 in fines after its drivers caused delays and missed stops during the first two months of the school year.

The bus company, First Student, has agreed to credit the account of the New Haven Board of Education in the amount of $66,667 per month for three months. In exchange, the school district will not press legal charges.

First Student has a $9 million-per-year contract with the school district to provide transportation to about 17,000 of the city’s students on some 150 buses, Chief Operating Officer Carey Paster said Tuesday. Under the terms of the contract, the company must pay a fine of $150 for every late arrival and $500 for every missed run.

“We have a pretty sizable contract with them, so we expect timely service,” said Catherine Sullivan-DeCarlo, a spokeswoman for the school system. “Getting kids to school on time is critical.”

Sullivan-DeCarlo said many of the company’s problems affected the city’s 1,000 magnet school students, many of whom are bused across town to attend their “schools of choice.” She said these problems left administrators scrambling to provide service.

The company got off to a rough start in the fall due to a two-month shortage of about 40 drivers, which resulted in late arrivals and, in some cases, missed runs, Paster said.

“We started at the beginning of the school year with a severe driver shortage,” he said. “Thus we were short a number of drivers, which caused havoc throughout the transportation system.”

Paster said the company underestimated the turnover rate; drivers expected to return to work after the summer break did not. First Student brought in drivers from other states and helped get them Connecticut licenses to meet the demand in the city.

“We recognize the problems and we worked within the school system, we worked out the fines and assessments with them,” Paster said. “So there are a lot of positives that came out of this.”

The school district hired a consulting firm to complete a $20,000 study of the transportation system.

Transportation Advisory Services, the consulting firm, suggested changes to drivers’ schedules and route maps that could result in $600,000 in further savings for the city, Paster said.

The firm made recommendations for the two weeks next summer before school begins: an aggressive planning process including daily meetings between school and company officials, supplemental administrative help in the transportation office and improved communication between officials and school principals.

TAS officials hope these recommendations will improve service and avoid similar problems at the start of the next school year. Paster said the company is now operating well, without major delays, and will take the advice of TAS next year to avoid problems in the future.

“We’re in real good shape right now,” Paster said. “We plan to get a proactive early start on the recruitment campaign, recognize the turnout rate, and our goal is to have a full complement.”