A 46 percent spike in spending on homeless services by Mayor Bill de Blasio’s administration over two years hasn’t produced cleaner and safer shelters, City Comptroller Scott Stringer said Wednesday as part of an analysis of the mayor’s 2017 budget plan.

“Money’s not the issue,” he said. “It’s more coordination, management and having the ability to get this done.”

The three main city agencies responding to the homelessness crisis are together spending $1.7 billion in the current fiscal year, with a 216 percent increase in funds toward prevention, diversion and anti-eviction programs since 2014, Stringer said.

A record number of people are living in shelters, including about 23,000 children, he said, referring to his December audit that found the city places families with children in shelters “plagued by rodents, mold, peeling paint” and broken windows. Some sites had weak security, including no guards and inoperable surveillance cameras, the report found.

The comptroller’s briefing was held before he learned of the stabbing at a Staten Island motel-turned-shelter that left a mother and two infants dead and a toddler injured.

Asked about Stringer’s budget critique, mayoral spokeswoman Amy Spitalnick accused the financial watchdog of “political grandstanding” and said the administration is “immediately and aggressively” addressing homelessness with a focus on prevention and moving people into permanent homes.

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“The homelessness crisis was created by years of disinvestment,” she said in a statement. “It takes sustained resources and smart management to address it, and that’s exactly what this administration is doing.”

Stringer’s formal response to de Blasio’s preliminary budget for the upcoming fiscal year also found larger future deficits than those estimated by the administration.

Stringer’s office forecasts a $2.7 billion gap in fiscal year 2018 and $3.8 billion each in fiscal years 2019 and 2020.

De Blasio’s team projected the gaps would be $2.3 billion in 2018, $2.9 billion in 2019 and $2.7 billion in 2020.

The comptroller’s calculation includes the elimination of $731 million in revenue from taxi medallion sales that he believes won’t happen amid the boom in e-hail services such as Uber.

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Spitalnick countered, “Out-year gaps are low and based on the city’s always-cautious revenue projections.”