Aquino said she and her two sons, Joshua and Baby James, will be staying with her elder sister Pinky for the meantime.
But she clarified she and Yap have not formally split up, and that they are just taking some time off to sort out their problems.
"I'm not saying that the marriage is over. In my heart, gusto ko the marriage to work for our kids. I'm not putting a period, I'm not saying this is the end of the road. I'm hoping and praying maayos namin lahat pero kailangan ko rin ng space," she told co-host Boy Abunda at The Buzz.
Aquino also said she still loves Yap no matter how rocky their marriage has been.
"I love him and he knows I still love him. I've never given him any reason to doubt my fidelity. I just want the same thing in return," she said.
"Hindi naman puwedeng ako lang ang nagmamahal… Ako lang umiintindi. It takes two for this marriage to work. I want him to make me feel I'm really (his) wife, that (he's) a responsible husband and a loving father and that this marriage has a future."
Recent reports came out that Aquino confronted and shouted insults at Mayen Austria, a female fan of Yap, who plays for the Purefoods TJ Giants. Aquino claimed the girl has been calling and sending her husband gifts.
A witness said the actress showed up at the residence of the Austrias in Valle Verde in Pasig City, and swore at Mayen and her mother.
Aquino had denied this.
In the interview with The Buzz, Aquino recounted what happened during the day of her encounter with Austria.
She said she was having lunch with Yap in their home when Yap's phone rang.
"When he answered, I heard a girl crying. I could hear their conversation because it was quiet in the house. Sinasabi noong girl, ginawa ko naman lahat... then James answered na kung ayaw sa ‘yo, 'wag mo pagpilitan ang sarili mo," Aquino narrated.
She said she asked Yap who called and he told her that it was Austria.
"Sabi ni James nagsabi sa kanya na iniwan daw ng isang guy and 'di alam ang gagawin.’ I asked him kung kilala niya iyong guy, he said no. So nagtaka ako, I said bakit ikaw ang iniiyakan?"
"I pointed out to James it was not proper. Baka she (Austria) was under the illusion that I'm not real, that I'm just a TV personality. So gusto ko puntahan para pakita na flesh and blood ako… tao ako... at misis ako," Aquino added.
And so she said she went to see Austria, who live two streets away from their house.
She said she rang the doorbell and Austria's mom came out.
"I said ma'am, I wanted to let you know, your daughter has been calling my husband and I'm not comfortable about it," she said.
"Never ako nagmura, never nanlait. Pinaramdam ko lang ang aking displeasure, siyempre asawa ako," said Aquino.
After narrating the incident, Aquino took the opportunity to apologize to Austria's mother.
"Mrs. Austria, on behalf of my family, hindi naman nga po kayo ang nanggulo sa asawa ko, kaya humihingi ako ng tawad sa inyo, pati kayo nadamay dito.
"Hindi ko gustong saktan kayo, ang kagalit ko po ay iyong anak niyo."
Aquino reiterated that her conversation with Austria's mom was "very calm the whole time."
She said it was just unfortunate that the incident has been blown out of proportion and turned into a major issue where her brother, presidential aspirant Senator Benigno "Noynoy" Aquino III, was dragged into.
"Sana po klaro sa inyong lahat. Hindi po kami nagpa-interview at nag-text tungkol dito. Pamilya nila. Napilitan lang akong magsalita dahil dinamay na ang kapatid ko."
Domestic not political issue
Aquino went on to defend her brother Noynoy on air even if she had been ordered by ABS-CBN Broadcasting Corp.'s management to refrain from talking about the presidential candidate during her entertainment shows to avoid being accused of bias.
She said she took offense that her brother was being "politically attacked" and dragged into the issue that does not even involve him.
"’Yong sinasabi nilang karapat-dapat ba sila sa Malacañang? 'Di naman ako ang binoboto n’yo, si Noynoy. Noong 'di approve si Noynoy sa way of life ko, 'di niya ko kinunsinti. He is of good moral character," she said.
Aquino said her brother has been counseling her and James on their marital problems.
"’Noy has been trying to help salvage our marriage," she said.
The love-hate relationship of Kris and James has always made headlines.
In 2007, they went through serious arguments after Yap was rumored to have had a romantic affair with Hope Centeno, one of the Belo Medical Clinic’s receptionists. Yap denied the rumors.