The report has 29 recommendations which it advises Kenya implement if it is to improve its election procedures.
Likewise, the EU Election Observer Mission recommended financial autonomy and infrastructure modernization of the electoral body to enhance its capacity to facilitate credible polls.
"Actions should be taken to strengthen the resilience of constitutionally independent institutions involved in elections, to preserve checks and balances in the electoral process", it added. Among of them being inclusive legal reforms, strengthening IEBC and review of the electoral system to improve inclusivity and women's participation in politics.
However, the report immediately sparked controversy.
During the presentation, the EU Chief Observer also noted that the Kenyan government was not prepared to receive the mission.
But Kenya's Ambassador to Belgium Johnson Weru disputed her assertion and accused European Union of breaching protocol.
But Mr Weru called Ms Schaake's actions "unprocedural and premature", saying it was she who had gone against the MoU between Kenya and the EU.
"Contrary to this assertion, the Government of Kenya has through diplomatic channels been in consultation with the EU-EUM on scheduling of the release of the report in Kenya in line with the stipulations in the MOU", he said.
"I call upon European Union to demonstrate that is committed to its agreements with its partners. Hon Schaake has personalised and intrumentalised a tool meant to improve electoral management", Weru said. "The report also went against the multilateral understanding under Article 8 and 96 of the Cotonou Partnership Agreement between European Union and 79 countries".
The Chief Observer of the EU Marietje Schaake, has presented the EU EOM final report on 2017 Kenyan general election and the repeat presidential repeat poll.
The mission further pointed out that there was; "intimidation of independent institutions by politicians from across the political divide, use of force by the police, attempts at restricting civil society and media, and abuse of state resources by both sides but mostly to the benefit of the national incumbent".
"This deepened concerns about political intimidation of the Judiciary".
Speaking with the Nation later, she said: "I can not speak for the government of Kenya, but it was made very clear they were not prepared to receive us at this time".
The team also notes that the opposition and its supporters assaulted and intimidated polling staff, attacked Independent Electoral and Boundaries Commission (IEBC) offices, and disrupted electoral preparations.
Schaake also observed that Kenya still remained divided and stated the need for a better democratic process and national healing.
"Criminal elements and gangs also contributed to the violence".
President Uhuru Kenyatta won a second term in an October rerun after his initial victory was nullified by the Supreme Court.
"The ruling appeared to prompt improvements in results transmission, verification and transparency in the fresh presidential election in October and thus raised standards of public service. However, the political environment deteriorated sharply", Schaake said.
"We were entirely prepared to travel to Nairobi this week to present the final report of our recommendations to the government of Kenya as well as to other important stakeholders, of course the most important being the people of Kenya".