With 90% of ballots counted, Mr. Kabila had 48% of the vote, while his closest challenger, opposition leader Etienne Tshisekedi, had 34%, Congo's independent election commission said, with full results expected on Friday.
Mr. Tshisekedi, a former prime minister, has rejected partial tallies released this week showing him trailing Mr. Kabila. His defiance has sparked street protests by his supporters in Congo and even European capitals. On Thursday, sporadic clashes between protesters and police broke out in the capital, Kinshasa. Supporters of Mr. Tshisekedi accused police of opening fire in front of the candidate's home, wounding several people. Attempts to reach Mr. Kabila and the police were unsuccessful.
Meanwhile, the British Broadcasting Corp. reported on Thursday that, in a matter believed to be related to a protest about Congo's political situation, passengers were evacuated from a tube station in central London after alarms were deliberately activated on a train.
Despite poor management and fraud allegations by the opposition, the international community has been restrained in its criticism of the vote amid concerns that wider unrest could erupt in the war-ravaged country.
On Thursday, the French, British and Belgian ambassadors held a joint meeting in Kinshasa to demand Mr. Tshisekedi call on his followers to remain calm when the results are announced. Speaking after their meeting, Belgian Ambassador Dominique Struye de Swielande acknowledged the election's flaws, but played down their impact.
"We work through observing missions, which in general observed that many aspects of the election went well," he said. "While recognizing deficiencies that could lead to controversies, we hope the truth will come out of the ballot box."
Election observers, opposition figures and diplomats have called on the election commission to release more-detailed election data. An estimated 32 million people were registered to vote for 11 presidential candidates and 18,000 candidates for 500 seats in Parliament, but allegations by the opposition and nongovernmental organizations of fraud and voter intimidation have marred results from Congo's provinces.
David Pottie, who led the Atlanta-based Carter Center's election-observation team, listed a series of critical problems with the election. Those included tens of thousands of lost and destroyed ballots, forced votes and the refusal of the election commission to release raw numbers from Congo's 63,000 polling stations, rather than the 11 sets of provincial-level results it has released.
Without raw data, Mr. Pottie said, it will be impossible for candidates and their supporters to verify the results and check their independent tallies with the official counts. "There was evidence of mismanagement of aspects of the election process right from the top," he said.
The electoral commission has promised to release those numbers after final results are announced. Then candidates will have 48 hours to file formal complaints with Congo's supreme court, but they will likely have to do so without the benefit of detailed polling data.
The stakes for Congo's election are high. The country has slipped in and out of civil war since 1996. And trouble here has often spilled into Congo's nine bordering countries, slowing development in the heart of the African continent. In a research note Thursday, the International Crisis Group warned that "Kinshasa will bear the brunt of the clashes, but violence could explode in other areas."
That threat of violence is tempering criticism from the international community, said Nyambura Githaiga, a Nairobi, Kenya-based researcher with the Institute for Strategic Studies, an African think tank.
"Caution is not a bad thing," said Ms. Githaiga. "These things can spiral out of control very quickly and if the opposition is riling things up and ready to go to the streets, the international community has to be the voice of caution."
The vote count is only the latest in a series of problems that have plagued the poll, the second since 2006, when Mr. Kabila won election. Mr. Kabila first assumed the presidency after his father, Laurent-Désiré Kabila, was assassinated in 2001.
Ahead of the election, Mr. Kabila pushed through election-law changes that replaced a runoff system and were seen to be favoring the incumbent. And he recently placed more than a dozen judges on Congo's Supreme Court—the last recourse for candidates unsatisfied with the election result.