District Judge Mattias Möller ruled that Azizul Raheem Awalluddin and his wife Shalwati Norshal were a flight risk, thus needed to remain in detention.
He however lifted the prohibition on communication, meaning their family and friends would finally be allowed to meet and speak with them, at the remand centre's discretion.
Kristofer Stahre, Shalwati's lawyer, said it while an early release hinted at an acquittal, the reverse was not a good sign.
"The gut feeling is that since the court has decided to keep them in jail, they might be found guilty of something," Stahre told reporters.
He added that there was still a chance Azizul and Shalwati might not be found guilty of all charges, which could mean a lighter sentence if they were convicted.
Shalwati was seen waving as she was lead out of court, and thanking her sisters plus the staff from the Malaysian Embassy and Tourism office that had attended the trial.
Azizul and Shalwati faced their 11th and final day of trial in the Solna District court here, with both sides submitting their closing arguments on Friday.
Prosecutor Anna Arnell attacked the parent's credibility, arguing Azizul changed his story mid-trial while Shalwati denied the charges, calling them fabrications by her children.
She admitted a few weaknesses in the interviews, saying the police had asked the children leading questions and conducted very long interviews, clocking in 26 hours.
Arnell urged the court for heavier prison sentences, in the range of two-and-a half-years for Shalwati and about two for Azizul.
She also suggested that the couple be expulsed from Sweden after serving their sentences.
Counsel Stahre argued that children were unreliable witnesses, as they either had motive to lie or were too young to give credible answers.
He noted that the second of four siblings, Ammar had been considering revenge against his parents, referring to the teenager's friend John Webb's testimony that Ammar was hateful towards his parents.
Azizul's lawyer Jonas Tamm questioned the vague timeframe of the charges, saying the uncertainty there meant the case would lean heavier on supporting evidence.
Tamm said factors that weakened the prosecution's case included: the leading questions asked by police, inconsistent evidence by the children, vague description of the offences, and a lack of substantial supportive evidence.
Sweden has outlawed corporal punishment since 1979, meaning Azizul and Shalwati face up to six years prison and a fine, if found guilt of hitting their children.
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