Schools in the city’s “Renewal” turnaround program have a little extra time and flexibility as they figure out how to add an extra hour of instruction to their schedules, according to an unusual joint letter Tuesday from the city schools chief and the heads of the teachers and principals unions.

The scheduling leeway comes after the principals union president sent his members a memo Friday saying the city had offered “no clear guidance” or “educationally sound proposals” as to how schools should squeeze in the additional learning time. That led to a series of meetings over the weekend and early this week between between Chancellor Carmen Fariña and the union leaders, according to principals union president Ernest Logan.

By Tuesday, they had settled on additional scheduling options for the extra instructional hour, which Mayor Bill de Blasio has promised will be coming to the low-performing schools in the turnaround program.

“We are united behind our common goal of working together to ensure that your schools have the tools and assistance necessary to succeed,” said the letter from Fariña, Logan, and United Federation of Teachers President Michael Mulgrew. A UFT spokeswoman said Wednesday that the union is still negotiating with the city over how teachers who choose to work during the extra hour will be paid.

Schools now have three additional options for how to rearrange their schedules to fit in the extra instructional hour alongside mandatory weekly teacher training and parent outreach, the letter said. One new option is to offer the equivalent of a daily extra hour through a combination of 40-minute sessions during the week and a three-hour session on Saturday.

The letter also said that schools would have two extra days to set their new schedules, which are now due Friday. A department spokeswoman said most schools have already submitted their new schedules, but ones that have not yet done so will get help from the city.

Logan said he sent last week’s memo out of frustration because he felt city officials had given principals confusing guidance about how to schedule in the extra time, which they appeared to come up with “willy nilly.” He said extending the school day is a major logistical challenge for school leaders, who must make sure that student transportation, school safety officers, and even crossing guards are all on board with the new hours. It did not appear the city had thought through all those logistics when it mandated the extra time at Renewal schools, he added.

“It’s not just about saying, ‘I’m going to extend the hour,’” he said. “You also have to say how are we going to do this.”

After he raised those concerns in the memo to principals, Logan said Fariña and Mulgrew agreed to meet over the weekend and early this week. He praised Fariña in particular for engaging in the talks, which he said led to “major, major progress.”

“The chancellor showed extraordinary leadership by personally getting involved in this,” he said.

Still, Logan suggested that the difficulties of adding the extra hour could point to an ongoing issue with the Renewal program.

De Blasio has said the city will diagnose and address the challenges at those 94 schools, and close or replace staffers at ones that fail to improve within three years. But principals at some of the schools have complained about receiving improvement recommendations from multiple officials in a way that is more confusing than helpful, Logan said. To be successful, the schools need more targeted support, he added.

“These schools need very careful intervention,” Logan said. “It’s not something that you can just throw everything at.”