The Metropolitan Transportation Authority should concentrate on improving the condition of its existing transit systems before plowing ahead with the second phase of the Second Avenue subway and other expansion projects, a watchdog agency said on Thursday.

In a report that called the authority’s priorities “misplaced,” the Citizens Budget Commission called for more emphasis on safety and increasing the capacity of the New York City subway system. The subways have been carrying heavier and heavier loads, exceeding six million riders on four separate days last month.

The analysis comes as the authority is seeking aid from Albany to cover a huge funding gap in its $32 billion capital plan for the next five years. The authority’s available money would cover only about half of the proposed spending, leaving transit officials to borrow heavily or find other sources of revenue to close the gap.

But Charles Brecher, the consulting research director for the budget commission, said the authority should reconsider its quest for additional money. “Let’s be sure we’re spending the money on the right things,” he said. Mr. Brecher said the authority was “paying too much attention to these new-start projects and not enough to fixing what we have and putting in modern communications and signals.”