Ms Knox was convicted, but later cleared, of Ms Kercher's murder following years of legal battles.
The European Court of Human Rights (ECHR) said on Thursday that there had been breaches of Ms Knox's rights leading up to a related conviction for malicious accusation.
Italian police alleged Ms Knox made false accusations against Congolese bar owner Diya "Patrick" Lumumba, knowing him to be innocent and in order to distract investigators away from her own responsibility.
But Ms Knox, now 31 years old, appealed on the grounds she was denied access to a lawyer and an independent interpreter, was slapped on the head and subjected to psychological pressure by Italian police.
The ECHR ruled that there had been a violation of Ms Knox's rights when her claims of ill-treatment in police custody were not investigated.
But the judges said the court did not have any evidence that Ms Knox was subjected to the "inhuman or degrading treatment" she complained about.
They also said that the Italian government had failed to show that Ms Knox's restricted access to a lawyer at police interview had not "irreparably undermined the fairness of the proceedings as a whole".
Judges further found that authorities had failed to assess the conduct of the interpreter assigned to Ms Knox and whether this had affected criminal proceedings against her.
The Italian government was ordered to pay Ms Knox 10,400 euro (£9,000) in damages and 8,000 euro (£7,000) for costs and expenses.
The body of Ms Kercher, a 21-year-old Leeds University exchange student, was found by police in the flat she shared with Ms Knox on November 2, 2007.
Officers discovered her throat was slashed and she had been sexually assaulted.
Ms Knox and her then boyfriend Raffaele Sollecito were arrested and later convicted of murder and sexual assault in 2009.
The couple maintained their innocence, insisting that they had spent the evening together at Mr Sollecito's home watching a film, smoking marijuana and being intimate.
Two years later, the Perugia Court of Appeal acquitted the pair of the more serious charges, but upheld Ms Knox's conviction for malicious accusation.
After three years in custody, Ms Knox was released and left Italy for the United States.
Ms Knox challenged the malicious conviction, but the Court of Cassation quashed her acquittal in 2013 and referred the case back to the Assize Court of Appeal.
That court re-sentenced her to more than 28 years in prison for complicity in sexual assault and murder, and three years for malicious accusation.
Ms Knox launched another appeal, and in 2015 she and Mr Sollecito were acquitted of sexual assault and murder by Italy's highest court, but Ms Knox was not cleared of the malicious accusation charge.
Rudy Hermann Guede, an Ivorian, is serving a 16-year sentence for Ms Kercher's murder.