Math test scores in D.C. public schools rose this year while reading scores remained essentially flat, officials reported Thursday, raising questions about how the city will meet ambitious goals for boosting student achievement over the next five years.

The District’s charter schools, which serve 41 percent of the city’s public school students, posted higher overall scores on the 2012 D.C. Comprehensive Assessment System than their counterparts in the traditional schools system, but their gains in math were smaller. Their reading proficiency rates, meanwhile, fell slightly.

Officials emphasized long-term trends at a news conference at Neval Thomas Elementary School in Ward 7 east of the Anacostia River. That school recorded double-digit gains in math and reading over the past year.

But citywide, progress was much slower.

In the District’s 123 traditional public schools, 46 percent of the students scored proficient in math, an increase of about 3 percentage points from the previous last year. Nearly 44 percent scored proficient in reading, an increase of 0.5 points.

“I can’t live or die by annual test scores,” D.C. Schools Chancellor Kaya Henderson said. “But I am completely and totally optimistic about results we are seeing.”

The small uptick in reading reverses two years of declines and is notable, Henderson said, because students and teachers were working with revised curriculum and tests that were aligned with more rigorous national standards.

Education experts believe schools across the country are likely to see students’ performance falter in coming years as national tests are rolled out that correspond to the tougher standards, which were adopted by all but a handful of states.

The city’s public charter schools posted a proficiency rate of about 55 percent in math, up a little more than 1 percentage point since last year.

But in reading, charter schools appear to have plateaued at about 49 percent, a number that has not risen significantly since 2009.

“We have to be honest and say the growth in reading has been smaller than we would like it,” said Brian W. Jones, chairman of the District of Columbia Public Charter School Board. “We can do better.”

He said that charter schools continue to outperform traditional public schools while serving a higher percentage of students from poverty.

The District must report test scores annually under the 2002 No Child Left Behind law, which set a controversial target that all children should pass grade-level tests by 2014.

This year, the District, along with Maryland and Virginia, obtained a federal waiver from that provision by offering alternative targets for improving performance.

The city’s new goal is to cut failure rates in half by 2017 so that 73 percent of students in public schools are proficient in reading and 74 percent are proficient in math.

Over the next two years, the city also will begin holding schools accountable for meeting targets in science.

This year, 40 percent of traditional public school students scored proficient on science tests, up 5 percentage points from the previous year. For charter students, the proficiency rate was 44 percent, down 1 point.

The city made impressive progress on test scores in 2008 and 2009, a feat that has not been repeated since. The city’s inspector general, aided by federal Department of Education authorities, has spent more than a year investigating whether some gains from that period were the result of cheating. The investigation continues.

D.C. education officials have said their progress over time is attributable to fundamental improvements to the curriculum and the teaching corps.

D.C. Mayor Vincent C. Gray (D) lauded “steady progress” the public schools are making and anticipated future results would show more dramatic gains as the city’s investments in early childhood education pay off.

Results released Thursday showed that by third grade, students who attended pre-kindergarten were slightly more likely to be proficient in math and reading. The difference was evident across racial and ethnic groups.

Gray said in a press statement that the gains are “proof-positive of the impact Pre-K participation is having on education in the District of Columbia.”