Two New York City charter schools risked thousands of city dollars with sloppy financial management, according to audit results released Wednesday by the city comptroller’s office.

Neither school was caught funneling money into illegal channels, but both showed signs of careless paperwork that could have led to the misuse of money, according to the comptroller’s report.

At Bedford Stuyvesant New Beginnings Charter School, an elementary school in Brooklyn, officials lacked written contracts for construction projects and wrote many checks for small amounts of money — possibly to avoid greater oversight that comes with spending larger sums of money. Officials at the other school, Merrick Academy Queens Public Charter School, made significant and undocumented changes to contracts.

“Ensuring that every dollar we spend on schools goes toward the education of the next generation must be our highest priority,” said Comptroller Scott Stringer in a statement.

These two schools are part of a series of charter school audits that the comptroller announced in 2014. The most anticipated is a review of Success Academy, the city’s largest charter network that educates 11,000 students.

A few months ago, Stringer announced results of the first charter school audit, of South Bronx Charter School for International Culture and Arts, which found that it overpaid its principal and could not account for purchased MetroCards.

Officials at the comptroller’s office gave little information about why those schools were chosen, other than to say they were selected based on criteria like geography, size, and publicly available data.

New Beginnings charter school released a lengthy response to the comptroller’s claims, agreeing with some recommendations and rejecting others. The school noted that they have improved practices since the audit began and said that information was not reflected in the final report.

“We see this omission as a missed opportunity to portray the current state of our school accurately, particularly after such a lengthy, 19-month audit,” reads the letter signed by Joseph Sciame, chair of the charter school’s board of trustees.