"The report is correct," Basescu said in a televised address.
"It notes the progress made over the past few months in making the Romanian judiciary more efficient and compatible with other European systems," he added.
"At the same time it points to enduring shortcomings that affect the credibility of the justice system and of Romania as a whole."
The Commission's report, released Wednesday, hailed the "significant steps" taken over the last year aimed at improving and modernizing the judiciary.
But it also stressed that more efforts were needed in order to fight widespread corruption.
"Several important high-level cases remain delayed in court for several years," said the report.
Basescu said he shared Brussels' critical assessment of the Supreme Court.
Lengthy proceedings could lead to indicted lawmakers and politicians getting off scot free thanks to a special statute of limitations provision, he said.
The European Union's executive arm has monitored reform efforts in Romania and neighbouring Bulgaria every year since they joined the EU in 2007 to ensure the judicial systems are credible and independent.
The main benefit of this monitoring had been it had ensured the independence of institutions such as the anti-corruption prosecutor's office and the general prosecutor's office, Basescu said.
They were no long subordinate to politicians "and have just one master, the law," he added.
Although both Romania and Bulgaria are hoping the Commission will end theri monitoring, Brussels hyas said a decision to this effect will be examined next year.