Ninety-seven percent of the votes favored statehood but voter participation was just 23% after opposition parties called for a boycott of what they called a "rigged" process in part over the ballot language.
Congress, the only body that can approve new states, will ultimately decide whether the status of the US commonwealth changes.
"It will be up to this new generation of Puerto Ricans to demand and claim in Washington the end of the current improper colonial relationship, and begin a transition process to fully incorporate Puerto Rico as the next state of the Union," Governor Ricardo Rosselló of the pro-statehood New Progressive Party said in a statement Sunday.
For Puerto Rico to become a US state, Congress would need to pass a statute laying out the transition process. If Congress does not pass a statute, Puerto Rico's status will remain as it is.
Options on the weekend referendum included remaining a commonwealth, becoming a state or entering free association/independence. Free association is an official affiliation with the United States. Typically it would include Puerto Rico still receiving military assistance and funding but the ballot says the terms would be agreed upon by the two countries as sovereign nations.
But the ballot's previous language prompted calls by opposition parties to boycott what they saw as a rigged vote.
Sunday's ballot was a revised version after the Department of Justice wrote to Roselló in April saying the referendum ballot at the time incorrectly omitted Puerto Rico's current commonwealth status as a ballot option, offering only statehood or free association/independence. The letter was published in the local newspaper El Vocero.
The previous ballot incorrectly claimed statehood was "the only option" for Puerto Ricans to secure their American citizenship. The DOJ in its letter pointed out that Puerto Ricans are US citizenship by birth, asking that the "potentially misleading" statement be removed.
The ballot was later changed to include "current territorial status" as an option, but the call for a boycott remained.
Fifty-four percent of voters in that referendum backed changing Puerto Rico's current territorial status. In a separate question, 61% chose statehood as the alternative, compared with 33% for the semi-autonomous "sovereign free association" and 6% for outright independence.
Some argued the results should have been considered a "no" since more than one-third of voters left the part about alternative status blank. Congress did not act on that referendum.
In 2012, around 1.8 million people voted -- a turnout of 77.5% -- but State Electoral Commission figures show that just 518,000 people (or 23% of eligible voters) voted in Sunday's referendum. According to the commission's numbers, 300,000 fewer people voted for statehood on Sunday than in 2012.
Hector Ferrer, leader of Popular Democratic Party, said eight out of 10 "stayed home" or "went to the beach" instead of voting.
"The governor lost, statehood lost," Ferrer said. "They lost 300,000 votes in four years."
Rosselló contested the commission's figures, telling CNN the electorate was 1.6 million -- meaning turnout was 33%.
In a statement, the governor said that he would travel to the US capital to speak with Congress, the White House, and other agencies regarding the referendum results.
"We will now take these results to Washington, D.C., with the strong support of not only a duly executed electoral exercise, but also of a contingency of national and international observers, who can attest to the fact that the process was fair, well organized and democratic," Rosselló said.
"From today going forward, the federal Government will no longer be able to ignore the voice of the majority of the American citizens in Puerto Rico. It would be highly contradictory for Washington to demand democracy in other parts of the world, and not respond to the legitimate right to self-determination that was exercised today in the American territory of Puerto Rico," he said.
What's Puerto Rico's current status?
Puerto Rico came under US control in 1898 after the Spanish-American War. It has its own governor and legislative body and it became a US commonwealth territory with its own constitution in 1952.
Its commonwealth status means Puerto Rico is subject to US federal laws, though island residents are exempt from some federal taxes.
Puerto Ricans have been US citizens since 1917, however, as residents of a commonwealth territory rather than a state they can't vote for president in the US general election. The territory has a nonvoting delegate in Congress, called a resident commissioner.
It also gets US military protection and receives federal funding from the government for highways and social programs, just not as much as official states receive.
What are the arguments for and against?
Roselló has argued that statehood for Puerto Rico could help the island's economy.
Puerto Rico declared a form of bankruptcy on May 3
, owing its creditors $73 billion.
Unemployment is high, holding steady about 11.5% since March
, and about 46% of the population of 3.4 million people live below the poverty level.
Popular Democratic Party Senator Jose Nadal Power wrote an op-ed in El Nuevo Dia last Monday
arguing that statehood was not the answer.
"This Sunday's plebiscite wastes millions of dollars and is not a good use of the time and energy we must devote to solving the fiscal and economic crisis of Puerto Rico. It lacks the backing of the United States federal government and comes at the worst possible time to solicit political concessions from Congress," he wrote.
Meantime Senator Juan Dalmau of the Puerto Rican Independence Party said on Twitter that
: "Including colony as an option in the plebiscite is a setback to the aspirations of decolonization and former governor Anibal Acevedo Vila of the Popular Democratic Party said on Facebook
that he would not be voting "as an act of conscience."
"Tomorrow, not voting is a form of voting. [the New Progressive Party] has lied about the "bonanza" of statehood and the supposedly devastating consequences of not asking for it," he said.